Payroll Help

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How to Fix an Incorrect Payroll

Available for: Patriot Payroll (Basic Payroll and Full Service Payroll).

Note for Full Service Payroll customers: Full Service Payroll is Patriot’s tax-filing plan, where Patriot handles federal and state payroll tax filings on your behalf. Some corrections — including payroll history entries and payroll edits — require you to contact Patriot Support before proceeding. Those steps are called out throughout this article.

Sometimes a payroll gets processed with incorrect information. Use the decision tree below to identify the best fix for your situation. Common examples of incorrect payrolls include:

  • Incorrect earnings or pay rate
  • A benefit deduction or employer contribution was applied incorrectly or missed entirely
  • An employee was taxed in the wrong tax jurisdiction
  • S-Corp owner health insurance contributions were missed at year end

Step 1: Has the Employee Already Been Paid?

If the employee has NOT yet been paid:

The best fix is to void the payroll and rerun it with the correct settings. Voiding and rerunning is the cleanest option because it keeps your payroll records and tax calculations aligned.

See: How to Void a Paycheck

If the employee HAS already been paid:

Continue to Step 2.

Step 2: What Needs to Be Corrected?

Identify which scenario below matches your situation to determine the best fix.

Scenario A: You paid an employee but forgot to record it in Patriot Payroll

Best fix: Add the missing payment through Payroll History.

Payroll History is a feature in Patriot Payroll that lets you record pay information for past pay periods that were not processed through the software. This keeps your payroll records and tax totals accurate without altering a previously processed payroll.

Full Service Payroll customers: The Payroll History link is not active by default on Full Service Payroll accounts. Contact Patriot Support to request that the Payroll History link be turned on before you proceed.

Scenario B: You need to add employer contributions for a past payroll

Best fix: Add the employer contributions through Payroll History.

Employer contributions — such as a 401(k) match or employer-paid health insurance premiums — typically do not change an employee’s net pay, so adding them through Payroll History corrects your records without requiring a payroll edit.

S-Corp owners: If you missed adding S-Corp Health Insurance for a greater-than-2% S-Corp owner and the January 10th year-end deadline has passed, you can still add the S-Corp Health Insurance contribution through Payroll History.

Full Service Payroll customers: Contact Patriot Support to request that the Payroll History link be turned on before you proceed.

Scenario C: You need to add or remove an employee deduction on a past payroll

Employee deductions — such as health benefit deductions or 401(k) contributions — that need to be added or removed after an employee has already been paid require a payroll edit.

A payroll edit is a manual correction made by Patriot’s payroll edit team to adjust a previously processed payroll. Payroll edits are requested by contacting Patriot Support (see Step 4: Request a Payroll Edit below).

Best fix: Submit a payroll edit request to Patriot Support.

Scenario D: The employee was taxed in the wrong jurisdiction

If an employee’s paycheck applied tax withholding for the wrong state or locality, the payroll record must be corrected with a payroll edit.

Best fix: Submit a payroll edit request to Patriot Support.

Before contacting support, update the employee’s tax jurisdiction in Patriot Payroll so that future paychecks withhold from the correct location.

Step 3: Is the Payroll in a Closed Tax Period?

A closed tax period is a quarter or year for which Patriot has already filed your payroll tax returns (such as Form 941, Form 940, or state equivalents).

  • If the payroll is NOT in a closed tax period: The correction can be made without filing amended tax returns.
  • If the payroll IS in a closed tax period: Amended tax returns will need to be filed. Keep in mind that changing a Q1 payroll after Q4 has already been filed will require amended returns for both Q1 and Q4.

Full Service Payroll customers only — Step 3a: Do you want Patriot to file your amended returns?

Full Service Payroll customers can request that Patriot file amended returns on their behalf. Amended return fees apply per quarter:

  • Q1 amended return: $100
  • Q2 amended return: $100
  • Q3 amended return: $100
  • Q4 amended return: $150

If you prefer to file amended returns yourself, you are responsible for submitting the corrected returns directly to the IRS and your state tax agency.

Step 4: Request a Payroll Edit

To request a payroll edit for Scenarios C or D above, email Patriot Support at support@patriotsoftware.com using the format below.

Email subject line:

PS number: XXXXX Payroll Edit Request

Email body:

I am requesting the following payroll edit(s) for [Company Name] [PS number]:

  • Pay date(s)
  • Full name of employee
  • Edits needed (list the name of the tax, contribution, or deduction exactly as it appears in your Patriot Payroll account)
  • Amount(s) to adjust
  • Additional details or clarification, if the categories above do not apply

(Repeat the above for each employee as needed.)

Full Service Payroll customers — if the edit is in a closed tax period, also include:

  1. Do you want Patriot to file amended returns on your behalf? (Yes / No)
  2. If yes, include the following acknowledgment: I agree to the amended return fees and acknowledge that my credit card will be charged at the time of the amended return filing.

[Your name]

Step 5: Verify Your Changes

Once Patriot’s payroll edit team completes your payroll edit request, you will receive an email confirmation. The corrected payroll information will appear in your Payroll Details report.

To verify the payroll edit in your Payroll Details report:

  1. Go to Reports > Payroll > Payroll Details.
  2. Set the Date range to the quarter start and end date. Note: some edits may be reflected using the last day of the quarter or year.
  3. Enter the Employee name(s) affected by the edit.
  4. Under Source, uncheck all options except Payroll Update.
  5. Check the Group by checkbox.

Click Run Report and confirm the corrected amounts appear as expected.

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