Should a farm S-Corp file Form 941 or Form 943 for shareholder wages?

For an S-Corporation that operates as an agricultural business, the determining factor isn't your business structure but rather the nature of the work being performed. Since you and your brother are performing agricultural labor on the farm, Form 943 would be the appropriate form to file. Form 943 is specifically designed for reporting wages paid to agricultural employees and the associated employment taxes. The fact that you're organized as an S-Corp doesn't change the agricultural nature of the work. As shareholders performing agricultural labor, you're considered agricultural employees for employment tax purposes. One advantage is that Form 943 is filed annually rather than quarterly like Form 941, which means less paperwork for you. You'll still need to make tax deposits according to the normal schedule, but the reporting is consolidated into one annual form.

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Has anyone dealt with switching from Form 941 to Form 943 mid-year? We've been filing 941 quarterly but just realized we should probably be on 943 as a farm S-Corp. Not sure if we should wait until January or make the switch now.

Anyone using QuickBooks to handle this farm S-Corp payroll situation? Does it know to generate the correct forms (943 vs 941) for agricultural businesses?

This is a great question that highlights the complexity of farm business taxation. As others have mentioned, Form 943 is indeed the correct choice for your situation since you're performing agricultural work, even though you're organized as an S-Corporation. The key point is that the IRS looks at the nature of the work being performed rather than just the business entity type. Since you and your brother are doing agricultural labor (feeding livestock, planting, harvesting, equipment maintenance), you're considered agricultural employees for employment tax purposes. One thing to keep in mind is that you'll still need to make employment tax deposits on the same schedule as Form 941 filers (monthly or semi-weekly depending on your deposit obligation), but you get the benefit of annual reporting instead of quarterly forms. Make sure to keep good records of your tax liabilities throughout the year since you won't be filing quarterly reports to track them. If you haven't already, I'd recommend confirming this with your accountant or getting a direct answer from the IRS to make sure you're set up correctly from the start.