I'm the sole shareholder and employee of an S-corporation. I handle my own payroll using Excel, file quarterly Forms 941, and make federal payroll tax payments through EFTPS.
I recently discovered that I may have incorrectly reported federal income tax withholding on my 2025 W-2 and Forms 941.
Here's exactly what happened in 2025:
- Annual gross W-2 wages: $60,000
- Monthly gross salary: $5,000
- Monthly federal income tax actually deducted from salary: $1,000
- Monthly Social Security withheld: $310
- Monthly Medicare withheld: $72.50
- Monthly net salary transferred to my personal account: $3,617.50
- Total annual federal income tax actually deducted from salary: $12,000
- Federal income tax withholding reported on my W-2: $37,560
- Additional federal income tax reported as withholding but not deducted from salary: $25,560
Where I made the mistake:
I intentionally paid additional federal income taxes through my S-corporation's EFTPS payroll tax account to cover my personal income tax liability on S-corporation profits.
I included those additional payments as federal income tax withholding on my quarterly Forms 941 and annual W-2.
However, I never reduced my salary payments by the additional withholding amounts. My regular net salary remained $3,617.50 per month.
At the time, I believed that because the additional taxes were paid to the IRS through EFTPS and reported on my payroll filings, they could be claimed as federal withholding on my W-2.
I now understand that this may not have been the correct treatment.
What I've verified:
- My four Forms 941 report a combined $37,560.50 in federal income tax withholding, essentially matching my W-2 Box 2 amount of $37,560.
- My Forms 941 report $46,740.50 in total annual payroll tax liability, including employer and employee Social Security and Medicare taxes.
- I've located bank statements and EFTPS payment records showing payments totaling $46,740.50 that match the reported quarterly liabilities.
- The payments were real, but I recognize that making them doesn't necessarily mean the additional $25,560 qualifies as employee wage withholding.
My current IRS situation:
The IRS issued a CP05A notice holding my 2025 personal income tax refund and requesting documentation supporting my wages and federal withholding.
The response deadline is November 26, 2026.
I don't have traditional payroll service paystubs because I handled payroll myself and transferred my net salary directly from my business bank account.
My questions:
- Can the additional $25,560 potentially be treated as employer-paid federal income tax or additional compensation to an S-corporation shareholder-employee? Would this require a wage gross-up?
- Would correcting this typically require Forms W-2c and 941-X? Are there restrictions on correcting prior-year federal withholding?
- If the additional payments should have been personal estimated income tax payments rather than payroll withholding, is there a process for correcting or transferring the payments?
- Given the pending CP05A notice, what is the appropriate way to explain the discrepancy and respond without making inaccurate claims about withholding?
- Is there anything specific in IRS guidance or tax law I should review before consulting an enrolled agent or CPA?
I want to correct this properly and ensure the IRS receives accurate information. This was an unintentional misunderstanding of how additional federal withholding should be handled for an S-corporation owner.
I'm not looking to avoid taxes or claim withholding that I'm not entitled to. The payments were made, and I'm trying to determine their correct treatment.
Any insight from tax professionals who have encountered a similar situation would be greatly appreciated.