Quarter-End and Tax Filing Resources

Be sure to download the Quarter-End Checklist to help you close out the quarter.

You may find several versions of tax returns in you Quarter-End tax package:

• The tax returns that you must file are located behind the cover sheet labeled Original Returns.
• Reference copies of your returns are included behind the cover sheet labeled File Copies. Please retain the reference copies of all tax returns in compliance with federal and state regulations.

State returns facsimiles:

A few states will not allow Paychex to reproduce their returns. If you must file any of these affected returns, we have enclosed a facsimile report with your tax package that includes the following message:

“Transfer this information to the return provided by the state. Do not file the facsimile.”

Follow these instructions to remit the return to the agency:

1. Transfer the information from the facsimile to the pre-printed return provided by the tax agency > sign the return > make a copy of the completed return for your files.
2.  If the return shows a balance due, enclose a check made payable to the name of the agency > write your ID number on the check.

Important note for Taxpay clients:

If you have any of the following situations for tax agencies on your payroll account:

• Tax agencies that do not allow Paychex to remit returns on your behalf.
• Paychex cannot remit returns because we do not have proper documentation of your agency ID or Power of Attorney.
• You have requested that Paychex not remit returns to a specific tax agency.
• You are considered non-Taxpay for these tax agencies.

Be sure to file the original return included in your tax package and refer to the non-Taxpay instructions in this document for the tax agency.

Paychex Flex^® – Access Quarter-to-Date, Year-to-Date Reports, and Employee Earnings Records
You can find many payroll, quarterly, and tax reports under Quick Reports, including:

Payroll Reports > Employee Earnings Records and Year-to-Date Reports
Tax Reports > Quarterly Report and Tax Return

Go to find and run Quick Reports.
For reports you access on a regular basis, you create and manage report sets.

Verify that your assigned identification (ID) numbers appear correctly on all returns. If any of the following information is incorrect, contact your Service Representative immediately:

• If an ID is missing, please print it in any applicable original return(s). In addition, please forward the ID number to your payroll contact.
• If your return shows "APPLIED FOR" but you have been assigned an ID number, white out "APPLIED FOR," and enter your ID number in any applicable original return(s). In addition, please forward the ID number to your payroll contact.

Paychex Flex^® – Update Missing Tax IDs
If you want to update missing federal, state, or local tax IDs in Paychex Flex, go to Learn how to update a missing tax ID or use these instructions.

Electronic Federal Tax Payment Service (EFTPS)

All employers should be making payments electronically on the EFTPS website. The only exception to this rule is that taxpayers who file Form 941 can send a check with the return if their liability is $2,500.00 or less for the quarter. Similarly, if the taxpayer is a Form 944 filer, they can remit taxes due with the return if their liability is $2,500.00 or less annually.

The IRS requires us to notify our Taxpay clients that although Paychex is designated as the Reporting Agent on Form 8655 (Reporting Agent Authorization), this does not relieve you from liability if tax payments and/or returns are not remitted by the due date. The IRS recommends that clients enroll in and use EFTPS to ascertain whether an agent has made all required deposits on time. Most state agencies provide ways for you to verify tax payments as well; contact your state agency for this information. Please be assured that Paychex makes every effort to remit your tax payments and returns on time. If any issues do arise, we work with you and the agency to resolve the situation.

Form 941 - Employer's Quarterly Tax Return

On the 941 return:

• Line 1, Number of Employees, must be completed for each quarter.
• If you do not have to file a Form 941 for one or more quarters in 2025, check the Seasonal Employer box on page 3, Line 18, and tell your Service Representative.

Taxpay clients: 

You will receive a reference copy of the return in your quarterly tax package that you should keep for your records. You may have an explanation for adjustment on lines 7 and 8 and/or Schedule B if required.

Non-Taxpay clients: 

Your quarter-end tax package will include a file-ready Form 941.

1. Verify your federal employer identification number (FEIN), name, and address.

• If the FEIN is incorrect, contact your Service Representative immediately.
• If your name and/or address are not correct, contact your Service Representative immediately. Cross out the incorrect information and clearly write in the correct information.

2. Verify that the amount on line 13a equals your total deposits for the quarter.

• If you have not deposited the amount shown on line 13a, contact your Service Representative before filing the return. You may be subject to an additional penalty for any overstatement of liability paid.

3. If you paid a deposit of $100,000.00 or more during the quarter or are a semi-weekly filer, file the enclosed Schedule B with your Form 941.

Note: If you believe you are a next-day or semiweekly depositor, but no Schedule B is enclosed, contact your Service Representative to confirm your federal deposit frequency.

4. If line 14 shows a balance due:

• Deposit the liability electronically.
• Payments can be made with the return only in the following circumstances:
  • If you have less than $2,500.00 of tax liability during the quarter (line 12 on Form 941). If you are not confident that your liability will be less than $2,500 deposit under the appropriate rules so that you won't be subject to failure to deposit penalties, or
  • If you are a monthly depositor and make a payment based on the Accuracy of Deposits Rule. This payment can be $2,500.00 or more.

See Publication 15 2025 (Circular E) Employer's Tax Guide > section 11, Depositing Taxes, for details. 

If you meet the requirements to make a payment with the return, enclose a check made payable to the United States Treasury with the return. Write your FEIN, "Form 941," and the tax period to which the payment applies on your check.

5. For first quarter, sign the return and mail it on or before April 30, 2025. Refer to Where to File Tax Returns for the correct address.

Fair Labor Standards Act (FLSA) Reminder

Commissions, certain bonuses, and other types of compensation may need to be accounted for when determining the overtime pay owed to an employee under the FLSA and state wage laws. To include commissions, bonuses, or other types of compensation in your overtime calculation, advise your Service Representative. If you are uncertain whether to do so, consult your attorney or accountant.

 We’ve also updated our State Tax Filing Resources site to make it easier for you to find what you’re looking for, by state.

Please note: The links available through this new feature may take an extra moment to load, depending on the resource.

The following states have changed their filing information, or are reminders about some needed state reporting. We've detailed this information on the State Tax Filing Resources site:

• Delaware– Employers need to make sure they are registered for Paid Leave and assign Paychex as a third-party administrator.
• Maine – Employers need to make sure they are registered for Paid Family & Medical Leave and assign Paychex as a third-party administrator.
• Michigan - If your business is in good standing, your 2025 Michigan SUI wage base will be reduced from $9,500 to $9,000 which could represent a significant savings in SUI taxes.
• Vermont – Report FTEs (full-time equivalent) for health care premium calculation and reporting on the quarterly SUI return. Instructions about how to update Paychex Flex are also included.

 For more detailed information about these and other state changes, go to the State Tax Filing Resources.