What happens when company switches me from 1099 contractor to W2 employee midyear? Tax implications?
So I've been working as a freelance physical therapist for about 3 years now, providing relief services to various clinics when their regular staff is unavailable. I'm completely independent - make my own schedule, set my own rates, pay all my own taxes, and don't receive any benefits or specific instructions on how to do my job. I basically email clinics and agree to pick up shifts as needed. I've always received 1099-NECs for my work as an independent contractor. With one particular clinic, I've been submitting invoices and they've been paying me as a 1099 contractor for most of this year. However, they're now claiming this arrangement "wasn't supposed to be that way" and that I should have been classified as a W2 employee all along. The weird thing is they did accidentally pay me as W2 for my very first invoice with them, but then switched to 1099 payments for the dozen invoices since then. Now they're saying they want to switch me back to W2 for all future payments. I asked if they could reverse that initial W2 payment from months ago and reissue it as 1099 to keep everything consistent, but they claim they can't do that. This presents a couple problems for me: #1) What happens when you receive both a 1099-NEC and W2 from the same company in the same tax year? I'm worried this will trigger an IRS audit and cause problems for me. #2) They're claiming I'm an employee based on some criteria that don't seem to align with the IRS guidelines. From my understanding, the IRS classification is based on behavioral/financial control and relationship factors (permanency, benefits, etc.), and my arrangement clearly fits the independent contractor definition. I really prefer keeping my 1099 status since it works better with my solo 401K situation. Any advice on how to handle this mid-year classification change?
32 comments


Yara Nassar
This is actually a common situation in your field, so don't worry too much about an automatic audit. The IRS sees mixed W-2 and 1099 income from the same company frequently enough. For your first question, when you file your taxes, you'll report both income types separately - the W-2 income goes on your 1040 form, while the 1099 income goes on Schedule C where you can deduct your business expenses. You'll pay self-employment tax on the 1099 portion only. The key is maintaining clear documentation showing which payments were which. Regarding your second question, worker classification is indeed based on the factors you mentioned. If you truly meet the criteria for independent contractor status (controlling your schedule, using your own methods, no permanent relationship, etc.), then you could potentially push back on their reclassification. However, many companies are becoming more cautious about contractor classifications due to increased scrutiny. For your 401(k) concern - you can still contribute to your solo 401(k) based on your 1099 income from this and other clients. You just can't include the W-2 income from this company in those calculations. Does this change affect a significant portion of your overall income? That would help determine how much this impacts your tax situation.
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Connor Murphy
•Thanks for the quick response! This particular client represents about 30% of my total income for the year. So the 1099 to W2 switch will definitely impact my solo 401k contributions. Would you recommend I try to negotiate with them more firmly about keeping me as 1099, or is it better to just accept the change and adjust my tax planning? And I'm still confused about whether having both types of income from one source in the same year might raise red flags with the IRS.
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Yara Nassar
•It's certainly worth having another conversation with them about maintaining your contractor status if it represents that much of your income. Prepare your case showing how you meet the IRS criteria for independent contractor classification - emphasize your control over when and how you work, that you serve multiple clients, and have business expenses. Having both types of income from one source in the same year isn't automatically a red flag to the IRS. What the IRS looks for is misclassification - either trying to treat employees as contractors to avoid payroll taxes, or contractors trying to avoid paying self-employment taxes. Since you have documentation showing the company initiated the change (not you), you're in a defensible position if questioned. Just keep all your communication with them about this classification change as evidence.
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StarGazer101
I went through something super similar when I was doing contract graphic design work! I found this amazing tool called taxr.ai (https://taxr.ai) that helped me make sense of my mixed income situation. I was getting totally confused about how to handle my taxes with some clients paying me as W2 and others as 1099, plus one that switched halfway through like yours. The taxr.ai system analyzed all my payment documents and gave me a clear breakdown of how to properly report everything. It even flagged potential issues with my contractor classification that could have caused problems during tax filing. What I really liked was that it showed me exactly how to maximize my retirement contributions with the mixed income types. It might help you figure out the solo 401k contribution limits based on your specific situation with the split payment types.
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Keisha Jackson
•How exactly does taxr.ai work with the solo 401k calculation? I'm in a similar situation where I'm getting both 1099 and W2 income from different sources, and I'm trying to figure out how much I can contribute to my solo 401k.
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Paolo Romano
•Not to be skeptical but does it actually handle situations specifically like this? I've tried other tax tools that claim to handle "complex situations" but then don't have specific guidance for contractor vs employee classification issues. Would be nice to have something that addresses this exact scenario.
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StarGazer101
•The solo 401k calculation feature is really helpful - it separates your income streams and automatically calculates your maximum allowable contributions based just on your 1099/self-employment income. It walks you through both the employee and employer contribution components specific to solo 401ks. For your specific question about contractor/employee classification, it absolutely handles this exact scenario. That's actually why I found it so valuable. It has a specific module for people with mixed income types from the same company and provides documentation guidelines if you need to explain the situation to the IRS. It even generates a customized explanation letter if needed for your tax return.
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Keisha Jackson
Just wanted to follow up - I tried taxr.ai after seeing this thread and it was seriously helpful! I was worried about my mixed income situation triggering an audit, but the system walked me through exactly how to properly document and file everything. The classification analysis tool confirmed I was properly classified as an independent contractor for most of my work and showed me which factors the IRS would look at if they questioned it. Even more valuable was seeing exactly how much I could still contribute to my solo 401k based on just my 1099 income. What really impressed me was how it generated a detailed report I could keep with my tax records explaining the mid-year classification change. Definitely gave me peace of mind about this complicated situation!
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Amina Diop
When I was dealing with a similar reclassification issue, I spent WEEKS trying to get someone at the IRS to answer my questions. Always on hold forever, then disconnected, or told to call back. Super frustrating! I finally discovered Claimyr (https://claimyr.com) which got me connected to an actual IRS agent in under 20 minutes. You can see how it works in this video: https://youtu.be/_kiP6q8DX5c The agent walked me through exactly how to handle reporting both 1099 and W2 income from the same company and confirmed that it's not automatically a red flag as long as you document the transition properly. They also explained my options for pushing back if I believed I was correctly classified as an independent contractor based on my working arrangement. It saved me so much stress compared to the endless hold times I was dealing with before. Definitely worth it when dealing with complicated tax situations like this!
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Oliver Schmidt
•Wait, how exactly does this work? I thought it was impossible to get through to the IRS without waiting hours. Is this some kind of special line or something?
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Natasha Volkov
•Sorry but this sounds like BS to me. I've tried every "trick" to get through to the IRS and nothing works. They're deliberately understaffed and overwhelmed. No way there's some magic service that can get you through in 20 minutes when regular callers wait for hours.
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Amina Diop
•It works by using a technology that constantly redials the IRS until it gets through, then it calls you and connects you directly when it has an agent on the line. It's not a special phone line - it just handles the tedious redial process that most of us don't have time for. I was super skeptical too! But the difference is they have systems that can keep redialing automatically when lines are busy, which is what most of us can't do manually. I spent over 3 hours on multiple days trying to get through before using this. The technology just automates the frustrating part so you don't have to sit on hold for hours or keep redialing yourself. You literally just get a call when an agent is on the line.
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Natasha Volkov
I need to come back and eat my words. After posting my skeptical comment, I was desperate enough to try Claimyr anyway because I had a time-sensitive issue with the IRS about my own contractor/employee status question. I was honestly shocked when I got a call back with an actual IRS agent on the line about 27 minutes later. The agent was able to confirm that having both 1099 and W2 from the same company isn't automatically problematic as long as there's a legitimate business reason for the change (like what the original poster described). The agent also gave me specific advice about how to document the change in classification to avoid any issues. Apparently this happens more often than I realized, especially in industries with a lot of contract/freelance work. I'm still annoyed at how hard it is to reach the IRS directly, but I have to admit this service actually delivered exactly what it promised.
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Javier Torres
One thing nobody's mentioned yet - you should consider the benefits side too. When they switch you to W2, they'll start withholding taxes, but they should also be paying half of your Social Security and Medicare taxes (7.65%). Plus, depending on the company, you might become eligible for benefits like health insurance, paid time off, etc. I went through this with a therapy practice I work with. Initially I was annoyed about losing the tax advantages of 1099 status, but after calculating everything, the employer-paid portion of those taxes plus the benefits I qualified for actually made the W2 arrangement financially better in my case. Also worth noting - if they're suddenly concerned about classification, they may have received advice from their accountant or attorney that your arrangement doesn't meet the legal requirements for contractor status. Companies can face significant penalties for misclassification, so they may be trying to correct what they now realize was a mistake.
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Connor Murphy
•That's an interesting perspective I hadn't fully considered. They haven't mentioned any benefits package though - as far as I can tell it's just the classification change without any additional perks. And since it's just fill-in work when needed, I'm not sure I'd qualify for benefits anyway. Do you think it's worth asking them if there would be any benefits associated with the W2 classification? That might make it more appealing if there's some upside beyond just the employer portion of FICA taxes.
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Javier Torres
•Absolutely ask about potential benefits! Even part-time W2 employees sometimes qualify for pro-rated benefits or access to retirement plans. The employer portion of FICA taxes is guaranteed (that's a legal requirement), but there might be other benefits they haven't mentioned. Another thing to consider is unemployment insurance. As a 1099 contractor, you generally can't claim unemployment benefits if the work dries up. But as a W2 employee, you'd potentially be eligible if they stop giving you shifts. This became a huge deal during COVID when many part-time workers suddenly found themselves without income.
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Emma Wilson
I'm a practice manager at a medical office and we recently went through this exact situation with our relief physicians. The reason many companies are making this change now is because states have been cracking down HARD on worker misclassification. In California (where we operate), the ABC test makes it very difficult to classify workers as independent contractors. Even if you meet the IRS guidelines, state laws can be stricter. Our accountant advised us to switch several providers to W2 status mid-year to avoid potential penalties. For our providers who were concerned about their solo 401k contributions, we worked out an arrangement where we slightly increased their hourly rate to help offset the change. Maybe your company would consider something similar?
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QuantumLeap
•This is a really important point. What state are you in, OP? Some states like California with the ABC test or Massachusetts with their strict independent contractor laws make it MUCH harder to qualify as a true independent contractor than the federal guidelines.
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Nia Jackson
As someone who's been through several classification changes over the years, I'd strongly recommend getting everything in writing from your employer about this switch. Ask them to provide a written explanation of why they're making the change and what criteria they're using to justify the W2 classification. This documentation could be crucial if the IRS ever questions the mixed income from the same source. It shows that the change was initiated by the employer based on their interpretation of classification rules, not some scheme to manipulate tax obligations. Also, don't forget that you can file Form SS-8 with the IRS to get an official determination of your worker status if you believe you're being misclassified. It takes several months to get a response, but it provides definitive guidance. Just be aware that filing this form might create some tension with your client if they find out. One more thing - make sure you're tracking all your business expenses from when you were classified as 1099. You can still deduct those on Schedule C for the portion of the year you were an independent contractor, which can help offset some of the tax impact of losing that status.
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Ava Martinez
•This is excellent advice about getting everything in writing! I'm dealing with a similar situation right now and hadn't thought about requesting written documentation from the employer about their reasoning for the classification change. Quick question - when you mention Form SS-8, how long did it actually take in your experience? I've heard it can take 6+ months and I'm wondering if it's worth filing given that timeline. Also, did filing it create any awkwardness with your client relationships, or were you able to keep it relatively low-key? The point about tracking business expenses is spot-on too. I've been keeping detailed records but wasn't sure how to handle the transition period. Good to know I can still deduct the 1099 portion on Schedule C.
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Sasha Reese
•In my experience, Form SS-8 took about 8 months to get a response from the IRS. That was pre-COVID though - I've heard it's even longer now due to processing delays. The determination letter I received was thorough and clearly explained their reasoning, but by the time I got it, the tax year was already over and I'd already filed my returns. Regarding client relationships - I didn't tell them I was filing it initially. The IRS contacts both you and the employer as part of their review process, so they found out anyway. It did create some tension, but honestly, if they're confident in their classification decision, they shouldn't have a problem with getting official confirmation. In my case, the IRS actually sided with me that I should have been classified as an independent contractor, which vindicated my position. The business expense tracking is crucial during these transition periods. Keep receipts for everything - vehicle expenses, equipment, supplies, even your phone bill if you use it for work. You can deduct the business portion for the months you were classified as 1099, which can significantly reduce your self-employment tax burden for that period.
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Andre Rousseau
This is a really complex situation, but you're not alone in dealing with mid-year classification changes. From a tax perspective, having both 1099 and W-2 income from the same employer in one year is actually more common than you might think, especially in healthcare fields. A few key points to consider: **Documentation is crucial** - Keep all correspondence with this employer about the classification change. This shows the IRS that you didn't orchestrate the change for tax benefits. **Your solo 401(k) contributions** - You can still maximize contributions based on your 1099 income from all sources (including the portion from this employer before they switched you). Just calculate it properly when you file. **Push back strategically** - Since this represents 30% of your income, it's worth having a professional conversation about maintaining 1099 status. Prepare your case using the IRS's behavioral control, financial control, and relationship factors. Emphasize that you work with multiple clients, set your own schedule, and don't receive training or benefits. **State law matters** - Make sure you understand your state's independent contractor laws, as they can be stricter than federal guidelines. If they insist on W-2 classification, ask about any benefits or rate adjustments to help offset the change. And remember, the employer portion of FICA taxes (7.65%) is now their responsibility, which does provide some financial benefit. Have you had a chance to discuss this directly with their HR or accounting department to understand their specific concerns about the classification?
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Dananyl Lear
•This is really comprehensive advice, thank you! I haven't had a direct conversation with their HR department yet - most of my communication has been through the clinic manager who handles scheduling. That's probably my next step. The point about state laws is something I definitely need to research more. I'm in Texas, which I believe is generally more business-friendly, but I should verify if there are any specific healthcare worker classification rules I'm not aware of. One question about the documentation - should I be proactive and send them something in writing outlining why I believe I meet the independent contractor criteria? Or is it better to wait and see what their formal response is when I push back on the classification change? I don't want to come across as confrontational, but 30% of my income is significant enough that I think it's worth making a case for. Also, when you mention calculating solo 401k contributions properly - does that mean I need to separate out just the 1099 portion from this client, or can I use my total 1099 income from all sources for the year?
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Amelia Dietrich
I'm actually going through something very similar right now with a healthcare facility where I do relief work! The mid-year classification change is definitely stressful, but I wanted to share what I've learned so far. First, regarding your solo 401(k) question - you can use ALL of your 1099 income from ALL sources for your contribution calculations, not just the portion from this one client. So even if they switch you to W-2, you can still maximize your solo 401(k) based on your total self-employment income from all your other clients plus the 1099 portion from this client before the switch. For the documentation piece, I'd recommend being proactive but diplomatic. I drafted a brief email outlining how my working arrangement meets the IRS independent contractor criteria (behavioral control, financial control, type of relationship) and sent it to their office manager. I framed it as "wanting to make sure we're both on the same page about the working relationship" rather than challenging their decision directly. One thing that helped in my situation was emphasizing that I work with multiple facilities, provide my own equipment, and have complete control over which shifts I accept or decline. The IRS really focuses on those control factors. Also, don't forget that if they do switch you to W-2, they'll be responsible for the employer portion of payroll taxes (7.65%), which does provide some financial offset even if you lose some of the tax benefits of contractor status. Have you considered getting a consultation with a tax professional who specializes in contractor classification issues? Given that this represents 30% of your income, it might be worth the investment to get professional guidance on your specific situation.
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PixelWarrior
•This is really helpful to hear from someone going through the same thing! I'm definitely feeling less alone in this situation now. Your point about being diplomatic but proactive makes a lot of sense. I think I'll draft something similar emphasizing the control factors - especially since I do work with multiple facilities and have complete autonomy over my schedule and methods. The fact that they initially paid me as W-2, then switched to 1099 for months, and now want to switch back actually seems to support that there's genuine uncertainty about the proper classification. I'm curious about your experience with the tax professional consultation. Did they provide specific guidance on how to handle the mid-year switch, or was it more general advice about contractor vs employee classification? And roughly what did that cost, if you don't mind me asking? I'm trying to weigh whether it's worth the expense given the complexity of my situation. Also, thanks for clarifying the solo 401k calculation - that's a huge relief! I was worried I'd lose a significant portion of my contribution capacity, but knowing I can still use all my 1099 income from all sources makes this much more manageable.
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Liam O'Reilly
I'm actually a tax preparer who sees this exact situation frequently, especially with healthcare professionals. The mixed 1099/W-2 from the same company in one tax year is NOT uncommon and won't automatically trigger an audit - the IRS is well aware that classification changes happen mid-year for legitimate business reasons. A few practical points from what I've seen: **On the tax filing side:** You'll report the W-2 income normally on your 1040, and the 1099 income on Schedule C where you can still deduct your business expenses for that portion. The key is maintaining clear records showing which payments were which and when the change occurred. **Solo 401(k) impact:** You can absolutely still contribute based on ALL your 1099 income from all sources - including the pre-switch portion from this client. Don't let them take away that significant tax advantage. **Your leverage:** Since you mentioned this represents 30% of your income, you have real negotiating power here. The fact that they accidentally paid you W-2 initially, then switched to 1099 for months, actually demonstrates there was genuine uncertainty about proper classification - which supports your case. **Documentation strategy:** I'd recommend sending them a professional email outlining how your arrangement meets the IRS independent contractor tests, but frame it as seeking clarification rather than challenging their decision. Emphasize your control over schedule, working with multiple clients, and lack of integration into their business operations. Given the dollar amount involved, this is definitely worth pushing back on professionally. Many companies make these changes out of overcaution rather than clear legal necessity.
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Roger Romero
•This is incredibly reassuring to hear from someone who sees these situations professionally! I've been really worried about potential audit triggers, so knowing that mixed income from the same company is common enough that it won't automatically raise red flags is a huge relief. Your point about framing the conversation as "seeking clarification" rather than challenging their decision is brilliant - I think that approach will help me maintain a good working relationship regardless of the outcome. And you're absolutely right that I have leverage here given the income percentage involved. One follow-up question: when you mention maintaining clear records showing which payments were which, what specific documentation would you recommend? I have all my invoices and their payment records, plus email correspondence about the classification change. Is there anything else I should be gathering or organizing now to make tax filing smoother? Also, from your experience, do you find that companies are usually willing to negotiate on this, or do they tend to stick with their decision once they've decided to make the change? I'm trying to gauge how hard to push back while still preserving the working relationship. Thanks so much for the professional perspective - it's exactly what I needed to hear!
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Samantha Johnson
•For documentation, you're already on the right track! Keep those invoices, payment records, and email correspondence - that's exactly what you need. I'd also recommend saving any communications that show your independence (emails where you decline certain shifts, negotiate rates, discuss working with other facilities, etc.). If you have any contracts or agreements that outline your working arrangement, keep those too. From my experience, about 60% of companies are willing to negotiate when presented with a well-reasoned case, especially if the worker can demonstrate they truly meet IC criteria. The other 40% stick to their decision, often because they've received legal advice to err on the side of caution. The fact that they've already switched you back and forth suggests they're genuinely uncertain, which actually works in your favor. One tip: if they do insist on W-2 classification, ask if they'd consider increasing your rate slightly to help offset the lost tax benefits. Many companies are willing to do this since they're saving money on their side by not having to pay contractor markup rates. It's often a win-win compromise. You're handling this exactly right - professional, documented, and focused on the facts rather than emotions. Good luck with the conversation!
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Chloe Robinson
This is such a helpful thread! I'm dealing with a similar situation as a freelance nurse practitioner where one of my regular clinics wants to switch me from 1099 to W2 mid-year. Reading through everyone's experiences, I feel much more confident about how to handle this. The documentation advice is spot-on - I've already started organizing all my communications with them about scheduling flexibility and rate negotiations to demonstrate my independent contractor status. One thing I'm wondering about that I haven't seen mentioned: if they do insist on the W2 switch, would it make sense to propose a trial period? Like maybe agree to W2 status for a few months while we both evaluate how it affects the working relationship? That way if it doesn't work out well for either party, we could potentially revisit the classification. Also, for those who have been through this - did the switch to W2 actually change how the company treated you day-to-day? I'm worried they might start trying to exert more control over my schedule or methods once they classify me as an employee, which would definitely not work with my current setup serving multiple facilities. Thanks to everyone who's shared their experiences - this has been incredibly valuable!
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Mila Walker
•Great question about the trial period approach! That's actually a really smart diplomatic strategy that could work well for both parties. It shows you're willing to be flexible while also giving you an "out" if the W2 classification starts interfering with your ability to serve multiple clients effectively. Regarding your concern about day-to-day control - this is exactly why the classification matters so much. In theory, if they're classifying you as a W2 employee, they would have the right to exert more control over when, where, and how you work. But many companies don't fully think through these implications when they make the classification change. I'd suggest being very explicit about maintaining your current working arrangement even if they switch you to W2. Something like: "I want to make sure we're both clear that my scheduling flexibility and ability to work with other facilities will remain unchanged regardless of how I'm classified for tax purposes." If they start trying to impose employee-style restrictions after the switch, that could actually strengthen your case that you should be classified as an independent contractor. The IRS looks at the actual working relationship, not just the paperwork. Your idea about the trial period could be a win-win - it gives them the compliance comfort they're seeking while preserving your ability to demonstrate that the actual working relationship hasn't changed. Definitely worth proposing!
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StarSailor
This whole thread has been incredibly insightful! As someone who works in healthcare administration, I see these classification issues constantly, and the advice here is spot-on. One additional consideration I haven't seen mentioned - if your company is making this change due to a recent audit or compliance review, they may be more rigid about sticking to their decision. But if it's just precautionary, you definitely have room to negotiate. Also, keep in mind that some companies are switching contractors to W2 status in anticipation of stricter enforcement from the Department of Labor, not just the IRS. The Biden administration has been signaling they'll crack down harder on misclassification, so some employers are being extra cautious. For your solo 401k situation, you might also want to consider whether this change affects your ability to establish a SEP-IRA or other retirement vehicles if you have significant 1099 income from other sources. Sometimes having multiple retirement account types can actually provide more flexibility than just the solo 401k. The key is documenting everything and maintaining your professional relationship regardless of the outcome. Healthcare is a small world, and you want to preserve those connections even if this particular arrangement changes.
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Sean Fitzgerald
•This is such valuable insight about the broader regulatory environment! I hadn't considered that the Biden administration's signals about stricter enforcement might be driving some of these preemptive classification changes. That actually explains why my clinic might be being extra cautious even though my working arrangement clearly fits the independent contractor criteria. Your point about the Department of Labor vs. IRS enforcement is really important too - I've been focused mainly on IRS guidelines, but I should probably research DOL standards as well since they can be different. The suggestion about SEP-IRA as an alternative is interesting. Since I do have substantial 1099 income from other clients, would a SEP-IRA potentially allow higher contribution limits than my current solo 401k setup? I'm not familiar with how those compare when you have mixed income sources. And you're absolutely right about preserving the professional relationship. Healthcare really is a small community, and I don't want to burn bridges over this even if I disagree with their classification decision. The diplomatic approach everyone has suggested seems like the way to go - make my case professionally but accept their final decision gracefully if needed. Thanks for the broader perspective on what's driving these changes industry-wide!
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