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 or pay slips, 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

Update Payroll Settings

If you need to edit yours or your employees’ work locations, update your bank checking account, or your state tax details, use the below steps:
  1. Select the Payroll section on the left
  2. Then select the More Actions button in the top right corner
  3. Select Payroll Settings
  4. Then select either Work Locations, Bank Checking Account, State Tax Details, or Payroll Setup Documents
    Payroll settings listing different options.
  5. If you select State Tax Details, then select the State you want to update 
    1. Inside the [State] Tax Requirements, select Edit next to any section, then select Save and Continue
      1. If there is no option to select Edit next to a section that needs to be updated, reach out to the Support team directly instead 
    2. Then select Back when you're finished updating and select Finish to submit the information 
  6. If you select Bank Checking Account, select Edit Details to confirm
    1. Re-enter your new Routing Number and Account Number, then select Save and Complete
    2. Once you receive your micro deposits in your bank account, repeat steps 1-5 to edit your Bank Checking Account
    3. Then enter the amounts for Test Deposit #1 and Test Deposit #2
    4. Select Validate, then select OK to verify your updated bank account details
    5. Once your updated bank details are verified, re-run payroll to pay your team members. 

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 6:30 pm ET on business days. Use the below steps to run a payroll:
If you've selected Check as the payment method for any employee, you will need to manually issue, and if needed, print and mail the check for the employee outside of FreshBooks.
  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.

State Tax Information

FreshBooks Payroll powered by Gusto uses Gusto’s tax payment system to ensure your state and municipal payroll taxes are paid on time. This requires having your state tax account numbers and appropriate third-party authorization during your FreshBooks Payroll setup.
State Tax Registration and Resources
Use Gusto’s state registration and resources to find state tax requirements for your specific state. Listed below are some popular states for quick reference:
A complete list of websites and phone numbers for all state tax agencies can be found at Gusto’s State Tax Agency or IRS list.
State Tax Exemptions
If there are any payroll taxes that your business is not required to pay, reach out to our Support team directly with the following information to have this applied to your FreshBooks Payroll account:
  • The specific name of the tax
  • The effective date for the tax exemption
  • The reason provided by the relevant tax authority for the exemption
State Unemployment Tax
If you have not registered for State Unemployment Tax with your state’s tax agencies, FreshBooks Payroll can still deduct an estimated amount based on the New Employer Rate for your listed state. Once you receive your state tax account number, update your State Tax Details in your Payroll Settings. The updated rate will be used when filing and paying state taxes, and a Reconciliation Payroll will be completed automatically to debit or credit your bank account based on the finalized amount of the tax liability.
If this information is not entered prior to your tax deadline dates, there may be penalties and interest for late payments. In some cases, state taxes will have to be paid by your business outside of FreshBooks.
Other Tax Related Information - Use the below links to review Gusto’s other tax-related information:


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 6:30 pm ET on business days.

How do I add more team members to my FreshBooks Payroll?
If you’ve hired new team members after you’ve already completed setting up FreshBooks Payroll, you can add them and input their payroll information using the below steps:
  1. Add a team member to your account using the Add Team Members steps here
  2. In the team member’s profile, under Payroll, select the Set Up button
    Team member profile with set up button under payroll section.
  3. Add in the employee’s information using the Employees steps here
  4. Once the team member’s payroll profile is set up, you can assign the team member a role and invite them to FreshBooks using Invite Team Members steps here.

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.
To adjust your information, select More Actions, then select Payroll Settings.

What happens to my expenses if I have FreshBooks Payroll powered by Gusto connected and an active bank connection?
If you’re currently using FreshBooks Payroll powered by Gusto, your payroll runs are automatically imported as expenses. If you also have a bank account connected via Bank Connections or Bank Reconciliation that is also the same account you use for payroll runs, any transactions with Gusto as the merchant will not be imported automatically to avoid duplicate expenses.
This is dependent on your bank connection partner formatting the merchant information correctly in order to stop duplicate Gusto expenses from occurring. Any expenses created manually or imported via CSV file will not be checked for duplicate Gusto expenses.

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.