How do I run FreshBooks Payroll?

• Historical Payroll
• Run Payroll for Employees
  • Check Payments
• Run Contractor Payments
  • Share Contractor Payment Receipts
• Review Payroll Runs and Contractor Payments
  • Review Payroll Runs
  • Review Contractor Payments
• FAQs

Historical Payroll

Before You Begin

• You’ve answered Yes to Have you paid employees in [current year]? while answering eligibility questions for FreshBooks Payroll
• Your FreshBooks Payroll setup is complete and approved for you and all active employees on payroll
• Quarter-to-date (QTD) pay stub information for each prior quarter for active and dismissed employees paid this year
• Individual pay stubs from the current quarter for active and dismissed employees
• Check date is the date the employee was paid, this date determines your payroll tax liability and will be the date you enter when reporting previous payrolls
  
   

  First Check Date	What's Required
  Q1 / January 1 - March 31	Every pay stub in the current quarter
  Q2 / April 1 - June 30	QTD amounts on the last paystub in Q1 (1/1 - 3/31) with a check date of 3/31 or earlier Every pay stub in the current quarter
  Q3 / July 1 - September 30	QTD amounts on the last paystub in Q1 (1/1 - 3/31) with a check date of 3/31 or earlier QTD amounts on the last paystub in Q2 (4/1 - 6/30) with a check date of 6/30 or earlier Every pay stub in the current quarter
  Q4 / October 1 - December 31	QTD amounts on the last paystub in Q1 (1/1 - 3/31) with a check date of 3/31 or earlier QTD amounts on the last paystub in Q2 (4/1 - 6/30) with a check date of 6/30 or earlier QTD amounts on the last paystub in Q3 (7/1 - 9/30) with a check date of 9/30 or earlier Every pay stub in the current quarter

Add Historical Payroll

1. In the Payroll section, next to the Submit your payroll history promptly for accurate tax calculations message, select Submit Info
   
   
2. In the Add dismissed employees section, select either:
   
   
   1. Add dismissed employee to add any employees that received a paycheck this year
      
      
      1. Enter the employee’s Legal First Name, Middle Initial, and Last Name
         
         
      2. Then enter the Social Security Number and Date of Birth
      3. Next, specify the Work Address, Hire Date, and Last Employed Date
      4. Then enter the employee’s Street Address, City, State, and Zip Code
         
         
      5. Next select the Save button
      6. Repeat steps 2a i-v until all dismissed employees have been added, then select Continue
   2. Continue if you have no dismissed employees for this year
3. In the Add your previous payrolls section, select the Add previous payroll button
   
   
   1. For the Check date, select a date that your employees were paid, refer to the table for closed quarters’ check dates and pay period dates in the Before You Begin section above
      
      
   2. Then select a Pay period start date and Pay period end date
   3. Next, select Save and Continue
   4. Then for the first employee, select the Add amounts link
      
      
      1. Next, specify the Regular wage and Regular hours worked
         
         
      2. If needed, select the Add bonuses, tips or commissions link to add additional details
      3. For deductions and contributions, this will need to be amended manually after you’ve submitted your historical payroll at the end of these steps
      4. Then select the Calculate tax amounts link, taxes will automatically be calculated and populated in the fields for you
         
         
      5. Review the tax calculations and correct any amounts that differ from tax payments that have already been made, then select Save
   5. Repeat step 3d i-v for each employee listed
   6. Earnings and taxes will now be updated with the correct Gross pay, select Save and continue
4. Repeat step 6 as needed for each payroll run this year until all are recorded in your list of this year’s payrolls
   
   
5. Then select the Review tax liabilities button
   1. Under each tax type, choose the liabilities amount from the dropdown that you’d like FreshBooks Payroll powered by Gusto to pay on your behalf
      
      
   2. Then select Submit
6. Next, select Finish
7. Gusto will pay your tax liabilities on your behalf, and debit your company’s bank account 2 days after you run your first payroll in FreshBooks Payroll. All your previously entered payroll runs from step 6 will now appear in your Payroll History list in FreshBooks Payroll. You can now process regular payroll runs.
   
   

Run Payroll

1. Select the Payroll section
2. Next, select the Pay… button and then select Employees
   
3. In the Pay Period section, choose an available period in the dropdown
   
   
4. Then select Continue
5. In the Hours and Earnings section, review your employees’ information
   
   
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
   
   
9. Select Submit Payroll to start processing your payroll, and your payroll run will appear in the Payroll History list. 

Check Payments

• If not using Bank Rec - All employee check payment expenses should be deleted to avoid duplicate expenses
• If using Bank Rec - All employee check payment expenses are money-out transactions that need to be reconciled, review How do I reconcile complex transactions in bank reconciliation? for next steps

Run Contractor Payments

1. Select the Payroll section
2. Next, select the Pay… button and then select Contractors
   
   
3. In the Pay Date section, choose the Pay Date
   
   
4. Then select Continue
5. In the Hours and Payment section, select a contractor
   
   
6. Contractors’ pay total are automatically set to $0, edit the Hours field, and if needed, the Bonus and Reimbursement fields
   
   
   1. Next, for Payment Method, select Check or Direct Deposit
   2. Any contractors that are left with a $0 payment will automatically be removed from the Review and Submit section later and not receive any payments
   3. Then select Confirm
7. Next, select Continue
8. In the Review and Submit section, review the Total Amount details and the Business Pays section as needed
   
   
9. Select Submit Payment to start processing your payments, and your contractor payment will appear in the Payment History list.

Share Contractor Payment Receipts

1. Select the Payroll section
2. Under Payment History, select the contractor payment
   
   
3. Under Business Pays on the Pay Date, select a contractor
   
   
4. The contractor’s payment receipt will be displayed, use your browser’s print dialog to download it as a PDF
5. Repeat steps 3-4 for each contractor as needed, then share the PDF with your contractors using any communication method you prefer.

Review Payroll Runs and Contractor Payments

If needed, under Payment History, select the payroll run or contractor payment to review the Pay Period information: 

Review Payroll Runs

• Cancel - If you need to cancel the payroll or payment while it’s in the  status
• Payroll Receipt - View a summary of the payroll run and download each team member’s pay stub as a PDF to share with your team member
• Employee Pay Stubs - Under Business Pays, select a specific employee to view their pay stub and download as a PDF as needed

Review Contractor Payments

• Cancel - Check the box off next to a contractor, select Bulk Actions, then select Cancel Payment if you need to cancel the payment while it’s in the Submitted status
  
  
• Payment Receipt - Under Business Pays, select any contractor to view and download the payment receipt as a PDF

FAQs

• Information is missing, incorrect, or a new signature is required
• Bank information is incorrect
• Employee with new state requires new documents to be signed

1. Add any contractors who have been paid this year in your Team Members
2. Once all previously paid contractors have been added, reach out to our Support team directly
3. In your ticket to Support, specify each contractor’s name, the amount, and the payment date for each payment made this year.

• Direct Debit Payments - Any transactions with Gusto as the merchant will not be imported as expenses to avoid duplicate expenses
• Check Payments - Any transaction for payroll runs that are check payments will be imported as expenses