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How do I manage my FreshBooks Payroll?

With your FreshBooks Payroll powered by Gusto account set up, you can manage your payroll settings, manage your employees, and access your tax filings as needed. 
 
If you're looking to run payroll, review How do I run FreshBooks Payroll? instead. 
 
 

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. 
 

Manage Team Members

To add additional team members to your payroll as employees, use the steps in Add Team Members to add them as Unassigned team members first. Once added, you can set them up as an employee on FreshBooks Payroll with the below steps.
If needed, you can invite the team member to work with you inside your FreshBooks account as well. This is optional and allows the team member to help you with running your business in FreshBooks, review What permissions can I assign to my team member? to learn more about what each role has access to.
 

Set Up Employees

Add team members as additional employees to FreshBooks Payroll, these can be added anytime after completing your FreshBooks Payroll setup. Add a new employee to your payroll using the below steps:
  1. Go to the Team Member section
  2. Then select the team member you want to add as an employee
  3. In the team member’s profile, under the Payroll section, select the Add to Payroll button
    Team member profile with add to payroll button.
  4. Add in the employee’s information using the Employees steps here
  5. Once the team member’s payroll profile is set up, you can start running payroll for this employee. If needed, you can assign the team member a role and invite them to FreshBooks using the Invite Team Members steps.
 

Manage Employees

Update your employees’ information when needed to ensure payroll runs smoothly, as well as dismiss employees using the below details.
 
Update Employees’ Information
To update an employee’s payroll information, including address, compensation, or taxes, use the below steps:
  1. Go to the Team Member section
  2. Then select the employee
  3. In the employee’s profile, under the Payroll section, select either:
    Team member profile displaying active on payroll with options to select.

    1. Personal Profile to update the personal details and/or address
    2. Work and Banking Details to update the work location, pay type, compensation, and/or banking information
    3. Federal Tax to update the federal tax details
    4. State Tax to update the state tax details
  4. Then select Save to finish and your employee's information will be updated.

Dismiss Employee
To mark an employee as dismissed, use the below steps:
  1. If the dismissed employee is not listed in your Team Members section in your FreshBooks account yet, add them as an team member first
    1. Once added in your Team Members section, add them to FreshBooks Payroll so their personal profile, work and banking details, federal tax, and state tax information is recorded
  2. In your FreshBooks account, select the ? icon in the top right corner, or go to the FreshBooks Support page directly
  3. Select the Ask Us button
    1. In FreshBot, enter in “payroll support”
    2. Then select Manage a Team Member
    3. Next, select Dismiss Employee
    4. Follow the instructions with the details of the employee you’d like to dismiss. An email ticket will be sent to our Payroll Specialists who will follow up with you.
 

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:
 

FAQs 

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.

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