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Run Payroll

To ensure your direct deposit recipients receive pay on payday, payroll must be processed by 8 PM PT on your due 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.

Run Payroll

To process payroll for W-2 employees:

  1. Log in to the Payroll section of your online SquareDashboard or the Square Payroll app > click Pay Employees > Run Payroll to enter or import your employees hours. Don’t worry, you will be able to review everything before you confirm the payment.

  2. within the Schedule Payment section, select the preferred speed for payroll processing. Choose between these options:

    1. If you’re running payroll ahead of your due date for submission, you can select the Fastest available option, which will get direct deposit payments to your team two business days from the day you submit payroll for processing. Note: You'll need to apply for two-day payroll in order to use this option.

    2. Select Regular pay day to have direct deposit payments scheduled on your regular cadence.

    3. Select Manual payments to issue physical checks to your team. Square Payroll will not issue checks on your behalf.

  3. Select the Payment Method you would like to use to pay your employee(s). You can pay your employee(s) manually or by their default payment method.

  4. 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 navigating to your Payroll Team tab and entering in their personal, tax filing, and bank account information.

  5. If you are using Square Timecards (or a supported third-party timecards application), enabled Tip Importing, Commission Importing with Square Payroll, or if you require your team to declare cash tips when clocking out or switching jobs, click Import time and wages to import your employee’s hours, tips, or commissions for the pay period.

  6. 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.

  7. 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.

    • Tips Already Paid: Amount tips paid out in cash. 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.

      • Alternatively, from the Shifts tab of your dashboard you can require your team to declare cash tips when clocking out or switching jobs. Note: This requires a subscription to Team Management.

    • Paycheck Tips: Amount of tips you want to pay 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 feature.

    • Sick Leave: Sick Leave hours used in the pay period. Will be turned on by default if you are using our Sick Leave feature.

    • Commissions: Commissions earned by employee(s) for the pay period. Will be turned on by default if you are using our Commission Tracking feature.

  8. Double-check that all information entered is accurate.

  9. Click Continue. If you’ve set up employee benefits or post-tax deductions, confirm deduction/contribution amounts and make any necessary edits. You can also add reimbursements if needed.

  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 this is your first time using Square Payroll, you’ll be asked to confirm pricing to complete the pay run. To accept, click Next.

  12. If you are paying employees by Printed Check, click “Print Checks” to download a PDF file of your employee checks.

Employees with a Square Payroll log-in will receive an email containing a link that will allow them to view their paystubs.

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 want to send a bonus separately, accidentally underpay or 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.

Two-Day Payroll

Two-day payroll allows you to submit payroll up to two business days from your team’s pay date, giving you more time to run payroll, off-cycle payments, and contractor payments. Learn more about how to apply for two-day payroll In our Support Center.

Note: Two-day payroll is not available for contractor-only payroll accounts at this time. Employers that pay both W-2 employees and 1099 contractors are eligible to apply for two-day payroll on their account.

Learn more about: Payroll

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