Square Payroll Amendment Service FAQ

The Square Payroll Amendment Service is a paid service offered to Square Payroll subscribers to assist them with correcting payroll tax forms that were submitted incorrectly.

In general, the following issues are supported as part of our paid amendments program:

• Correction to employee information, such as name or Social Security number (SSN);
• Addition of missing payroll history from a prior payroll service provider that was not submitted on time to be included in filings;
• Deleted pay runs;
• Addition of pay runs or tips recorded outside of Square Payroll (subject to approval by our team);
• Moved pay runs (for example, moving a January run or stub to December of the prior year); and
• Correction of an error in reported benefits.

In general, the following amendments are not supported as paid amendments:

• Amendment of tax forms filed prior to joining Square Payroll;
• Amendment of tax forms filed by a third party;
• Amendments for concurrent payroll (running payroll through two payroll companies at the same time);
• Amendment for Families First Coronavirus Response Act (FFCRA) runs, including amendment of Form 941 or 944 for the Employee Retention Credit (ERC);
• Amendment of tax forms as “final” filings; and
• Amendment for issues that are not supported in-product as a feature by Square Payroll.

Note: this is not a comprehensive list. If the case does not fall into one of the above categories, our team will review it and determine whether it is eligible for our paid amendments program.

The Amendments team can assist with correcting most federal and state quarterly and annual payroll tax forms that are filed automatically as part of the Square Payroll subscription service, including corrections to Forms W-2 and 1099-NEC. Review the list of the tax forms filed by Square Payroll.

Note: there are some exceptions we will be unable to support due to state regulations or other circumstances.

In the event that your original tax filing is unsuccessful due to an invalid account number or similar issue, you will need to resubmit the filing once the issue has been corrected. Learn more about how to make payroll withholding tax filings.

The Amendments team may be able to file on your behalf through this service and will make this determination before sending an estimate.

If your case is determined to be ineligible for the Square Payroll Amendment Service, you will need to seek amendment services through an accountant or other tax professional. You may also amend your tax forms directly with the relevant tax agencies.

Form 1099-NEC is a payroll tax form used to report non-employee compensation, such as payments to independent contractors. Form 1099-K is a non-payroll tax form that differs from Form 1099-NEC and is not supported by the Square Payroll Amendment Service.

Learn more about Form 1099-K tax reporting information and how to make corrections.

Before submitting your amendment request, confirm that Square Payroll has the most up-to-date information from you, including any missing payroll. Employee profiles should be complete and accurate, and benefits should be activated, if applicable. This review helps to ensure that your future tax filings will be accurate.

Learn more about making updates and corrections in Square Payroll.

If you have enabled an online account within their profile, employees have the ability to update their personal and tax information through their Square employee dashboard or through the Square Team App.

If you want to edit an employee’s personal and/or tax information, including name, address, or SSN:

• Go to Staff > Payroll > Payroll Team in your online Square Dashboard.
  1. Select the employee whose information needs to be updated.
  2. Change the personal and/or tax information as needed.
  3. Click Save.

If you edit an employee’s tax information, any changes to tax withholding will be reflected on the subsequent pay run.

For detailed instructions, see:

• Add Employees to Square Payroll
• Add Independent Contractors to Square Payroll

If you accidentally made an error processing payroll, you may be able to cancel the pay run. You’ll have until one hour before the deadline for processing to cancel the run. The deadline for canceling a pay run is 7 p.m. PT.

To cancel a pay run:

1. Go to the History & Reports section of your Payroll dashboard.
2. Select the run you want to cancel, then click Cancel.

Note: If you have processed multiple runs in a given day, you will need to cancel the pay run at the top of your history first and work down from there, canceling them one by one, until you get to the run you need to cancel.

If the run has already been sent and you accidentally overpaid an employee, contact us so we can assist with additional options.

To add missing payroll to the current tax period (before tax filings take place), you will need to run an off-cycle payroll payment.

To add missing payroll information to a prior tax period, we require an earnings report with the following details:

• Pay date
• Gross pay
• Federal income taxes withheld
• FICA/Social Security tax
• Medicare tax
• Any applicable state taxes
• Any deductions (pretax, post-tax, and garnishments) withheld from employees

Ensure that benefits are activated for employees who received or contributed to benefits in the affected tax year. In addition, all former and current employees for the affected tax year need to have complete employee profiles.

For detailed instructions on obtaining payroll reports from your prior provider, if applicable, see:

• Find Payroll History From Your Previous Provider
• Switching Payroll Providers

If you need to correct benefits reported in a prior tax period, provide the following information in your inquiry:

• Benefit type (such as 401k or Section 125 health insurance)
• Contribution date
• Employee and employer contribution amounts

Confirm that the benefit has been activated on the affected employee’s profile. Learn more about how to add existing employee benefits.

Note: S-Corp health insurance premiums for the current year are requested by Square Payroll at year end.

Reach out to our Customer Support team for steps on how to resolve this.

You can request an estimate by logging in to your account and contacting us to express your interest in the Square Payroll Amendment Service.

Provide a detailed description of the issues with your tax forms. Our team will review your request to determine which tax forms need to be corrected and provide you with an estimate of costs and lead time.

Some cases are not eligible for the Square Payroll Amendment Service due to unsupported tax situations or other circumstances. Availability of our amendment services is subject to change.

Since each case is unique, our Amendments team will review your request and provide you with an estimated cost of service based on tax forms to be amended, case complexity, and other factors. Your final cost of service may differ from the original estimate if there are any changes in complexity or the number or type of tax forms that need to be corrected.

Estimates will expire 14 days after being issued.

We are able to reissue the estimate, but the estimated delivery date and service costs may differ from the original estimate.

Invoice payment is due when you receive your invoice with the draft amended tax forms attached but before they are finalized and submitted to the applicable tax agency. No payment is due or made at the time you accept the estimate.

Payment of your invoice is treated as approval of your amendments and acknowledgement of any additional tax, penalties, and interest due or any refund indicated as such on your amended tax form.

If an invoice remains unpaid, we will send past-due notices with a required date of response approximately 2-4 weeks after the invoice is originally sent. If we do not receive a response from you by the date indicated, we will cancel your amendments.

If you later decide that you would like us to file your amendments, you may pay your balance due at any time and we will reopen your case.

An estimated date of completion is included on each estimate. This does not include time to file, which may take additional time depending on filing method and case volume.

There may be delays if we are missing required information, do not have access to your online payroll tax account, or for any other reason we are unable to prepare or file your corrected tax forms.

No. We are unable to accommodate requests to expedite amendments.

We recommend that employees who need amended W-2s file an extension for their personal taxes. Employees may also need to pay estimated taxes to avoid penalties and interest.

To determine whether an extension is required for your state, contact the state directly.

Because they are prepared manually by the Amendments team (outside of Square Payroll automated tax filings), most amended tax forms will not appear on your Square Dashboard. In most cases, the forms you see listed on your Tax Forms page are your original tax filings. If the original form was not filed for any reason, it will continue to appear as “Not Filed” on your Tax Forms page.

Drafts of your amended forms are typically attached to your invoice or may be sent via email. All forms sent as attachments are password-protected using your FEIN with no dashes or spaces.

Amended Forms W-2 and W-2c may be available on your Square Dashboard, depending on the circumstances of your amendment. The text in your invoice or email will indicate where your drafts are available and provide instructions for viewing the forms.

We are not always able to provide timely updates when forms are filed, but in general, we will file approximately 2-4 weeks after your invoice has been paid.

We are not always able to provide timely updates when amended tax forms are filed, but in general, we will file approximately 2-4 weeks after your invoice has been paid. At times, circumstances beyond our control may result in longer processing times than anticipated.

Once your invoice has been paid, our Amendments team will file your amended tax forms.

Most amended state and federal tax forms will indicate the amount due or the amount to be refunded. For example, on Form 941-X, this amount will appear on line 27.

Note: state or federal agencies may calculate additional penalties and interest due on any tax you owe as a result of your amendments.

Payment of your invoice is treated as approval of your amendments and acknowledgement of any additional tax, penalties, and interest due or any refund indicated as such on your amended tax form.

You are responsible for payment of any amounts due. If you have any questions about the calculated balance due or overpaid on your amendments, contact Square Support before paying your invoice.

For general support with making electronic tax payments, review how to make payroll tax payments. The IRS and state agencies may also allow you to make a payment by check or other method.

According to the IRS, the preferred method of payment is EFTPS. For more information, go to EFTPS.gov, or call EFTPS Customer Service at 800-555-4477 or 800-733-4829 (TDD) toll free. Additional information about EFTPS is also available in Publication 966.

Here are additional payment instructions for some common federal forms:

• Forms 940 and 941:
• If paying electronically, visit IRS.gov/Payments.
• If paying by check or money order, mail your payment along with Form 940-V or 941-V, which are payment vouchers included when you download Form 940 or Form 941, respectively, from the IRS for the appropriate year. The mailing address for each form is listed in the form instructions.
• Form 941-X:
• To pay by credit or debit card, go to IRS.gov/PayByCard. Your payment will be processed by a payment processor who will charge a processing fee.
• If you pay by check or money order, make it payable to “United States Treasury.” On your check or money order, be sure to write your EIN, “Form 941-X,” the calendar quarter you corrected (for example, “Quarter 2”), and the calendar year of the quarter you corrected.

For payment instructions for a specific state agency, we recommend that you contact the state directly.

Square does not have any insight into the refund processes for state or federal agencies. If you have questions about the status or amount of your refund, we recommend that you reach out to the tax agency directly.

Here are refund instructions for some common federal forms:

• Forms 940 and 941:
• Depending on the circumstances of your amendment, the Amendments team will check either “Apply to next return” or “Send a refund.” The IRS may apply your overpayment to any past due tax account shown in our records under your EIN regardless of the box checked on your amended form.
• If the amount of your overpayment is less than $1, the IRS will send you a refund or apply it to your next return only if you ask for it in writing.
• Form 941-X:
• Depending on the circumstances of your amendment, the Amendments team will check either “Adjusted employment tax return” or “Claim” on page 1. The IRS may apply your overpayment to any past due tax account that is shown in our records under your EIN regardless of the box checked on your amended form.
• If the amount of your overpayment is less than $1, the IRS will send you a refund or apply it to your next return only if you ask for it in writing.

We do not have any insight into the processing time for state or federal agencies. If you have questions about the status of your tax payment or refund, we recommend that you reach out to the tax agency directly.

Most amended data is processed directly within your Payroll account. Follow the instructions for Square Payroll reports to pull a custom report that will include any modifications made.