Run Payroll

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To ensure your direct deposit recipients receive pay on payday, payroll must be processed by 8 PM PT on the first business day following the end of your pay period (4 business days before the employee pay date). For more info on Square Payroll’s payment schedule and holiday exceptions, visit Square Payroll Payment Schedule.

These instructions are for paying W-2 employees. Learn how to Pay Contractors Through Square Payroll.

To run payroll for employees:

  1. Confirm your pay period and pay schedule. If this is your first time running payroll through Square Payroll and you need to update your pay schedule, click the edit button next to your pay period on the Payroll overview page or learn how to edit your payroll period.
  2. On the Payroll home screen, click Run Payroll to enter or import your employee’s hours. Don’t worry, you will be able to review everything before you send pay!
  3. Your employees must have their information entered for them to be able to be paid. If they have not entered this information, you can submit this info on their behalf by clicking “Enter tax info” and entering in their personal, tax filing, and bank account information.

    Note: Direct deposit employees must have a bank account linked to be paid through Square Payroll.

  4. If you are using Square Point of Sale’s timecards or a supported third-party timecards application, click Import Timecards to import your employee’s hours worked for the pay period.
  5. If you are not using timecards, enter the number of hours worked and any additional dollar amount earned (if applicable) for each employee into the appropriate columns:
    • Rate: The employee’s hourly wage.
    • Regular Hours: Number of hours worked at regular hourly wage.
    • Overtime: Overtime hours worked (1.5x the hourly wage).
    • Additional: Additional wages associated with the pay period, such as commissions. These amounts will be taxed as income and included in the employee net pay.
  6. Click the + icon next to Gross Pay and check the appropriate box(es) if you need to pay your employees for the following:
    • Double: 2x the hourly wage.
    • Cash Tips: Amount in cash tips paid. This amount should already have been paid to your employee and will not be sent in your pay run. Declaring cash tips ensures accurate tax reporting and documentation. Employee taxes will be calculated for these amounts and withheld from the employee’s pay.
    • Paycheck Tips: Tips paid out to your employee(s) for the pay period. This amount will be paid to your employee(s) through Square Payroll.
    • PTO: PTO hours used in the pay period. Will be turned on by default if you are using our Paid Time Off and Sick Leave feature.
  7. Double-check that all information entered is accurate.
  8. Click Continue. If you’ve set up employee benefits or post-tax deductions, confirm deduction/contribution amounts and make any necessary edits.
  9. If this is your first time using Square Payroll, you’ll be asked to confirm pricing to complete the pay run. To accept, click Next.
  10. You will be taken to a screen containing a detailed breakdown of the pay run and the bank withdrawal. Click Confirm Withdrawal to approve and process the payroll for the current pay period.
  11. If you paying employees by Printed Check, click “Continue to Printed Checks”.
  12. On the Print Checks screen, click Print All Checks to download a PDF file of your employee checks.

Employees with a Square Payroll log-in will receive an e-mail containing a link that will allow them to view their pay stubs.

Payroll debits appear separately on your bank statement from card payment credits and debits processed through the Square app.

Learn how to run payroll for employees with post-tax deductions and garnishments.

Off-Cycle Payments

We know that sometimes you need to pay your employees outside of your typical payroll schedule. If you accidentally underpay an employee, forget to pay one of your employees, or pay your employees on an irregular schedule, you can do so by making an off-cycle payment at no extra cost after you send your first scheduled pay run.

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