How do I run and manage payroll with FreshBooks Payroll?

Once your FreshBooks Payroll powered by Gusto account is set up, you can run payroll and review payroll information.
FreshBooks Payroll currently supports 4-day payroll processing (4-day ACH). All pay runs must be processed 4 business days prior to the payout date.

Payroll Section

Payroll details, including pay stubs, can be accessed by selecting the Payroll section. From here, you can find the below information:
Payroll section with a run payroll button at the top.
  • More Actions
    • View Payroll Reports - Go to the Reports section to review your Payroll Journal report
    • View Tax Filings - Review tax filings and payroll-related documents for your business
      • Check off the box(es) next to any form, select Bulk Actions, then select Download PDF to download copies anytime
    • Payroll Settings
      • Work Locations - If needed, add additional business and work locations
      • Bank Checking Account - If needed, update your bank account and verify your deposits
      • State Tax Details - If needed, review, edit, and submit tax requirements for each state
      • Payroll Setup Documents - If needed, review signed documents or sign outstanding documents as requested
  • Run Payroll - Run a payroll cycle for your team
  • Payroll History - Each Payroll Run is listed with its Pay Period, Pay Date, Total Payroll, Type and Status
    • Year - Select the dropdown to switch years, up to 6 years maximum
    • Pay Period Details - Select any Payroll Period to review the details of the payroll, including pay stubs
      • Business Pays - Select any employee under Business Pays to download that employee’s pay stub
      • Payroll Receipt - While reviewing a Pay Period, select the Payroll Receipt button to view a summary of the payroll run, and use your browser’s print dialog to save as a PDF if needed
Payroll Statuses
  • Submitted - The payroll run has been submitted to Gusto, business bank debits have not been initiated yet
  • Processing - The payroll run is currently being processed, business bank debits have been initiated
  • Paid - The payroll run has completed and employee direct deposit payments have been initiated

Run Payroll

Run a regular payroll based on your business’ pay schedule. The deadline to submit payroll runs is 4 business days prior to payout, by 3:30 pm PT on business days. Use the below steps to run a payroll:
  1. Select the Payroll section
  2. Then select the Run Payroll button
    Run payroll button.
  3. In the Pay Period section, choose an available period in the dropdown
    Pay period section with dropdown to choose a pay period.
  4. Then select Continue
  5. In the Hours and Earnings section, review your employees’ information
    Hours and earnings section with list of employees and their earnings.
  6. If needed, select an employee to edit their Hours, Additional Earnings, Reimbursements, and Payment Method, then select Confirm
  7. Next, select Save and Continue
  8. In the Review and Submit section, review the Business Pays and Debits, as well as Employee Take Home sections as needed
    Review and submit section with details of payroll run displayed.
  9. Select Submit Payroll to start processing your payroll, and your payroll run will appear in the Payroll History list.
If needed, under Payroll History, select the payroll run to review the Pay Period information. You can also select either:
Pay period of the payroll with a summary of all payroll information displayed.
  • Cancel - If you need to cancel the payroll while it’s in the Submitted status
  • Payroll Receipt - View a summary of the payroll run
When the payroll run is successfully marked as Paid, your employees will receive their direct deposit payments and their pay stubs by email.


When can I cancel a payroll run?
The option to cancel payroll is only available while the payroll is in Submitted status. While in the Submitted status, payroll must be canceled before the payroll deadline of 3:30 pm PT on business days.

Why didn’t my payroll run?
If you received an error trying to submit your payroll where Payroll information is required, this can be due to any of the below:
  • Information is missing, incorrect, or a new signature is required
  • Bank information is incorrect
  • Employee with new state requires new documents to be signed
To adjust your information, select More Actions, then select Payroll Settings.

How can I run an off-cycle payroll run?
If you need to run an off-cycle payroll outside of your regular pay schedule, please reach out to our support team to run an off-cycle payroll for you. Include specific information like employee names, work periods, payment dates, any deductions and contributions, and payment details in your request.
How do I switch from using FreshBooks Payroll to the Gusto app instead?
If you need additional functionality outside of what FreshBooks Payroll can offer, you can use the Gusto app instead. To migrate your FreshBooks Payroll account to Gusto app directly, please reach out to our support team to send in a request from your FreshBooks account. This will also transfer your billing subscription for the FreshBooks Payroll add-on to Gusto instead.