My employer stopped withholding federal taxes from paychecks due to Workday system issues
Title: My employer stopped withholding federal taxes from paychecks due to Workday system issues 1 I'm currently working for a state government agency and we switched to Workday for our payroll about 7 months ago. Since then, there's been a major problem - my employer has told us that because of how Workday was implemented, they can't withhold federal taxes from our mid-month paychecks. This has been going on for 7 months straight now, and I'm really starting to worry about the tax implications. I've never had this happen before and I'm concerned about what might happen when I file my taxes next year. What kind of repercussions am I looking at for not having these federal taxes properly withheld for such a long period? Will I end up owing a huge lump sum? Are there going to be penalties? Also, if there are penalties involved, is there any way to push those back onto Workday or my employer since this was their system error? I don't think it's fair that I might get penalized for something completely out of my control. Has anyone dealt with something similar or know what my options might be?
22 comments


Hunter Hampton
15 This is definitely a concerning situation, but try not to panic too much. Let me break this down for you: When federal taxes aren't withheld properly, you'll likely owe the full amount of those taxes when you file your return. The main concern is potentially facing an underpayment penalty if you end up owing more than $1,000 when you file. You have a few options to mitigate this situation now: 1. Increase withholding on your end-of-month paychecks to compensate for the mid-month shortage 2. Make quarterly estimated tax payments directly to the IRS to cover the shortfall 3. Check if you qualify for any safe harbor provisions (if you pay at least 90% of current year tax or 100% of last year's tax through withholding) As for placing responsibility on your employer or Workday - while your employer is technically responsible for proper withholding, the ultimate tax liability always falls on the taxpayer. You might request that your employer cover any penalties that result from their system error, but they're not legally obligated to do so. I'd recommend documenting everything related to this issue and consulting with a tax professional about your specific situation.
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Hunter Hampton
•7 Thanks for the breakdown. Do you think I should try to calculate what I'll owe now and start making payments, or wait until the end of the year? And what about the employees who might not even realize this is happening - does the IRS ever go after the employer in cases like this?
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Hunter Hampton
•15 I definitely recommend calculating your shortfall now and taking action immediately rather than waiting until tax time. You can use the IRS Tax Withholding Estimator on their website to figure out approximately how much you're short each pay period, then either increase your withholding on the end-of-month checks or make quarterly estimated tax payments. Regarding other employees, the IRS generally holds individual taxpayers responsible for their own tax obligations. While employers can face penalties for failing to withhold and deposit taxes properly, those penalties are separate from individual liability. The IRS won't typically absolve individuals of their tax responsibilities even if the employer made errors. That said, if multiple employees are affected, a coordinated approach to addressing this with management might help get a better resolution for everyone.
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Hunter Hampton
18 Hey, I went through something similar last year with my company's transition to Workday. After spinning my wheels trying to get answers from HR for weeks, I finally used taxr.ai (https://taxr.ai) to analyze my pay stubs and tax situation. It helped me understand exactly how much federal tax I was missing and what I needed to do to fix it. The tool basically looked at my pay stubs, calculated the proper withholding that should have happened, and showed me exactly how much I needed to adjust my W-4 on my remaining paychecks to make up the difference. It also gave me a breakdown of potential penalties I might face and how to minimize them. Honestly way more helpful than anything my company provided.
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Hunter Hampton
•9 How accurate was it? I'm worried about making adjustments based on some random online calculator and then still ending up with a tax bill next April.
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Hunter Hampton
•12 I'm curious - does it handle state taxes too? My situation is even more complicated because I live in one state but work in another, and this Workday mess has affected both my federal and state withholdings.
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Hunter Hampton
•18 The accuracy was surprisingly good. It matched what my accountant later calculated almost exactly. The difference was taxr.ai did it in minutes rather than me waiting two weeks for an appointment and paying a consultation fee. I was able to adjust my W-4 with confidence and ended up within $200 of my actual tax bill at year end. It definitely handles state taxes too. I actually had a multi-state situation as well since I moved mid-year, and it properly accounted for the different state tax rates and rules. It even flagged that I needed to file a part-year resident return in both states, which I wouldn't have realized on my own.
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Hunter Hampton
12 I just wanted to follow up about my experience with taxr.ai after seeing it mentioned here. I was skeptical at first (who isn't with tax stuff online?), but I gave it a try last weekend. Super glad I did! It identified that my employer wasn't just messing up federal withholding but also incorrectly calculating my state tax withholding across two states. The system walked me through exactly how to fill out a new W-4 and gave me specific numbers to put in the "extra withholding" field to catch up before year-end. I took this to HR yesterday, and for the first time, they actually understood the issue clearly! Apparently several other employees had the same problem but couldn't explain it well enough for HR to fix it. Now they're addressing it company-wide.
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Hunter Hampton
23 Have you tried getting through to the IRS directly to ask about this? I was in a similar situation (not with Workday, but with missing withholding) and spent WEEKS trying to get through to someone at the IRS who could give me straight answers about penalties. Finally tried Claimyr (https://claimyr.com) which got me through to an IRS rep in about 20 minutes. There's a video showing how it works here: https://youtu.be/_kiP6q8DX5c I was totally prepared to wait on hold for hours, but their system held my place in line and called me when an agent was ready. The IRS agent I spoke with gave me the exact penalty calculation formula and confirmed I could request a first-time penalty abatement since I had a good filing history. Also found out that my employer could potentially face separate penalties for not properly withholding, which was interesting info to bring back to my HR department.
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Hunter Hampton
•5 Wait, how does this actually work? Sounds like some kind of IRS line-cutting service which seems sketchy. Does the IRS actually acknowledge this service?
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Hunter Hampton
•8 I'm extremely skeptical about this. Why would I pay for something to talk to a government agency I'm already entitled to speak with for free? Sounds like a scam to me.
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Hunter Hampton
•23 It's not line-cutting at all. The system essentially automates the hold process for you. Think of it like having someone else sit on hold instead of you having to do it yourself. The IRS doesn't "acknowledge" it because they don't need to - from their perspective, it's just another caller waiting in the queue. I had the same reaction initially about paying to talk to a government agency. But after spending literally hours on multiple days trying to get through and always getting disconnected, I valued my time more than the service cost. It's basically the difference between potentially wasting an entire day repeatedly calling and waiting vs. going about your normal routine and getting a call when someone's actually available. Not a scam - they don't get paid unless you actually connect with an IRS agent.
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Hunter Hampton
8 I have to admit I was completely wrong about Claimyr. After posting my skeptical comment, I decided to try it anyway out of desperation since I kept getting disconnected from the IRS phone line after waiting 45+ minutes. Using the service, I got connected to an actual IRS representative in about 35 minutes without having to actively wait on the phone. The agent confirmed that I could submit Form 843 (Claim for Refund and Request for Abatement) to request relief from penalties due to my employer's payroll system failure. She also explained exactly what documentation I needed from my employer to support the claim. This was information I couldn't find anywhere online and would have had no way of knowing without speaking to someone directly. Honestly worth every penny just for the time saved and stress reduction.
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Hunter Hampton
3 Has anyone brought this up with your state labor department? This seems like it could actually be a violation of labor laws in some states. When my previous employer messed up payroll tax withholding, our state labor board got involved and forced them to provide affected employees with free tax preparation services that year and cover any resulting penalties.
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Hunter Hampton
•19 Curious about this too - what state are you in? I'm in Washington and I'm not sure if our labor department would consider this their jurisdiction or not.
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Hunter Hampton
•3 I'm in California, which tends to have stronger labor protections than many states. The key was that our employer had told us in writing that taxes would be withheld correctly, so when they weren't, it was considered a violation of our employment agreement. For any state though, it's worth checking. Most labor departments have free consultation services where you can call and ask if this falls under their jurisdiction without filing a formal complaint. The advice I received was incredibly helpful and led to a resolution that saved everyone affected hundreds or thousands of dollars in tax penalties.
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Hunter Hampton
10 Hey, might not be directly solving your problem, but I think the IRS has this first-time penalty abatement program you could look into if you do end up owing penalties. My friend used it last year when she had a similar withholding issue (different situation, but same outcome of owing a bunch at tax time). She got all the penalties waived because she had a clean tax history for the previous 3 years.
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Hunter Hampton
•17 This is actually really good advice! I work at a tax prep office (not a professional, just admin) and I see our preparers request this for clients all the time. The IRS is surprisingly willing to waive penalties for first-time issues, especially when it wasn't directly your fault. Just make sure to request it specifically - they won't offer it automatically.
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NebulaNinja
Document everything! I went through a similar Workday implementation disaster at my federal agency job. Here's what I wish I'd done from day one: 1. Save every paystub showing the missing federal withholding 2. Get written confirmation from HR/payroll about the system issue (email works) 3. Document every conversation about this problem with dates and names The key thing people aren't mentioning is that you should immediately start making quarterly estimated tax payments to avoid the underpayment penalty. Even if your employer eventually fixes this, you're already 7 months behind. Use Form 1040ES and make payments for Q3 and Q4 at minimum. Also, push your HR department hard on this. Seven months is way too long for a "system issue" - at this point they should be manually calculating and withholding the correct amounts even if Workday can't do it automatically. I'd escalate this to your union rep if you have one, or consider filing a complaint with your state's department of labor. The silver lining is that employer payroll failures like this are exactly the kind of situation where the IRS will often grant penalty relief, especially with good documentation showing it wasn't your fault.
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Miguel Ortiz
•This is incredibly helpful advice, especially about the quarterly payments. I had no idea about Form 1040ES - I've always just had taxes taken out automatically so this is all new territory for me. Quick question though - when you say "manually calculating," do you mean HR should be able to override the Workday system entirely? Our HR keeps saying their hands are tied because the system won't let them enter different withholding amounts. Is that just an excuse or could that actually be a technical limitation?
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Mei-Ling Chen
•That's likely just an excuse from HR. While Workday is a comprehensive system, payroll administrators absolutely have override capabilities for situations like this. They can manually adjust withholdings, add supplemental deductions, or even process manual paychecks outside the system if needed. What they're probably not telling you is that manual overrides require more work and documentation on their end. It's much easier for them to say "the system won't let us" than to admit they don't want to deal with the extra administrative burden. I'd suggest asking HR specifically: "What manual override options have you explored with Workday support?" and "Can you provide documentation from Workday stating that manual tax withholding adjustments are impossible?" Put the burden on them to prove they've exhausted all options. In the meantime, definitely get started on those quarterly payments. The IRS doesn't care about your employer's system limitations when it comes to your tax obligations.
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Ethan Anderson
This is a frustrating situation that unfortunately more government agencies are experiencing with Workday implementations. As someone who works in tax compliance, I'd recommend taking immediate action on multiple fronts: First, calculate your federal tax shortfall using your most recent paystub. Take your gross pay, subtract pre-tax deductions, then multiply by your effective tax rate (you can estimate this from last year's return). This will give you a rough idea of what should have been withheld. Second, file Form 4868 when tax season comes if you need more time to gather funds - this gives you an extension to file and can help avoid failure-to-file penalties even if you still owe. Third, consider approaching this collectively with other affected employees. When multiple people are impacted by the same system failure, agencies are more likely to find solutions quickly. You might also want to contact your state's ombudsman office if you're a state employee - they often have more leverage with agencies than individual complaints. The good news is that the IRS has several penalty relief programs specifically for situations like this where the taxpayer made good faith efforts but was prevented from proper compliance due to circumstances beyond their control. Just make sure you're documenting everything and taking proactive steps now rather than waiting until tax time.
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