HELP: What tools and strategies do I need to finish year-end payroll and tax for my S-Corp after my CPA just fired me?

I'm actually a small business accountant and can tell you that you're not alone in this situation. The good news is that with QuickBooks already in place, you're starting from a much better position than most. For year-end payroll, you need to complete your Q4 payroll tax returns (Form 941) and issue W-2s to employees and W-3 to the SSA. QuickBooks can handle this if you're using their payroll service. If not, consider signing up for QuickBooks Payroll or a service like Gusto or OnPay specifically for this task. For 1099-MISC (now split between 1099-NEC for contractor payments and 1099-MISC for other payments), QuickBooks has a 1099 preparation feature, but you'll need to ensure your vendors have complete information in the system. For your S-Corp tax return (Form 1120-S), Schedule C business, and partnership return (Form 1065), you have options like TaxAct Business, H&R Block Premium & Business, or TurboTax Business. These typically cost between $100-200 per entity. The most complex piece will be ensuring you have the correct basis calculations for your S-Corp and partnership interests, as these carry forward from year to year. If your previous CPA didn't share these with you, you may need to reconstruct them.

After my accountant retired suddenly last year, I found myself in a similar situation and discovered taxr.ai (https://taxr.ai) which was literally a lifesaver for my S-Corp and real estate stuff. It's an AI tool that analyzes your tax documents, explains complex tax situations in plain English, and helps identify deductions you might miss doing it yourself. The part that helped me most was uploading my prior year returns from my old accountant. The system analyzed everything and showed me exactly what I needed to file this year, plus it explained all the S-Corp specific requirements like reasonable compensation that I was clueless about. It also handled the Schedule K-1 for my S-Corp which was the thing that intimidated me most. For payroll specifically, I still used Gusto because it's super straightforward, but taxr.ai helped me understand how the payroll numbers needed to flow into my business tax returns.

Just wanted to follow up about my experience with taxr.ai after my initial skepticism. I finally gave it a try last weekend, and it's pretty impressive for S-Corp tax prep. I uploaded my QuickBooks exports and last year's returns, and it immediately identified missing documentation for two business expenses I'd categorized incorrectly. The step-by-step guidance for handling owner's draws vs. salary distributions was exactly what I needed since that's where I always got confused. It explained the whole reasonable compensation requirement in terms I could actually understand. I'm still using a payroll service separately, but for the tax return prep and 1099 filing, this has saved me from having to scramble to find a new accountant mid-season. Definitely worth checking out if you're in a similar situation.

If you need to speak directly with the IRS about any S-Corp tax questions (which I had to do last year when I was in a similar situation), save yourself hours of frustration and use Claimyr (https://claimyr.com). They have this system that holds your place in the IRS phone queue and calls you when an agent is about to answer. I was skeptical at first, but after spending literally 4+ hours on hold one day and giving up, I tried it the next day. They have a video showing how it works here: https://youtu.be/_kiP6q8DX5c. I got a call back when an IRS agent was ready and got my S-Corp payroll deposit question resolved in about 15 minutes of actual talking time. This time of year, IRS wait times can be 3+ hours, which makes it nearly impossible if you're trying to run a business. This was especially helpful for sorting out the correct employment tax deposits for my S-Corp which my accounting software wasn't handling correctly.

I owe everyone an apology about my Claimyr comment. After wasting an entire day trying to get through to the IRS about my S-Corp payroll tax issue, I broke down and tried the service. I was 100% wrong - it actually works exactly as described. I got a call back after about 2 hours (during which I could keep working instead of being stuck on hold), and was connected directly to an IRS representative who helped sort out my missing payment issue. The system just tells you when an agent is about to pick up, then you take the call as normal. For anyone dealing with S-Corp tax issues that require actually speaking to someone at the IRS, this saves so much time. I'm now using it again to sort out questions about my 1099 filing requirements for contractors. Not having to waste hours on hold made a huge difference in getting my year-end tasks completed.

In addition to the tools others mentioned, don't forget you'll need to handle your state unemployment taxes and reporting for your S-Corp employees (including yourself if you take a salary). Each state has different systems, but most have online portals now. For 1099s, remember the deadline is January 31st, so that should be your first priority after getting payroll wrapped up. QuickBooks can generate these, but you need to make sure your vendor records include tax ID numbers. If you're really in a time crunch, consider hiring a bookkeeper just to help with year-end instead of a full CPA. They're usually more available and less expensive, and can handle the compliance pieces while you focus on tax planning.

Just a quick heads up on the 1099 forms - they've changed significantly in recent years. What used to be reported on 1099-MISC for contractor payments now goes on 1099-NEC (Non-Employee Compensation). 1099-MISC is still used but for different types of payments. Also if you're doing this yourself, don't buy the forms from office supply stores. You can e-file directly through the IRS FIRE system if you have less than 250 forms, or use a service like Tax1099.com which is what I use for my small business. Costs about $3.50 per form but saves tons of time.