Once your FreshBooks Payroll powered by Gusto account is set up, you can import historical payroll and run employee payroll and contractor payments as needed.
Historical Payroll is used for businesses who transfer from one payroll provider to FreshBooks Payroll powered by Gusto after the start of a year to ensure year-end tax filings are up to date and accurate. Historical payroll includes inputting information to determine how much has been calculated and paid for each tax and each employee for the current year.
Every January, our payroll partner Gusto will be generating and submitting year-end tax filings. Gusto will also be generating year-end employee forms for team members, including any employees who were dismissed this year.
Previous payroll history is entered right after your onboarding, and before you start running your first payroll in FreshBooks.
Before You Begin
Before you start the process of importing your historical payroll into FreshBooks Payments powered by Gusto, make sure you review or have ready the following:
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
To begin adding historical payroll to your FreshBooks Payroll, use the below steps:
In the Payroll section, next to the Submit your payroll history promptly for accurate tax calculations message, select Submit Info
In the Add dismissed employees section, select either:
Add dismissed employee to add any employees that received a paycheck this year
Enter the employee’s Legal First Name, Middle Initial, and Last Name
Then enter the Social Security Number and Date of Birth
Next, specify the Work Address, Hire Date, and Last Employed Date
Then enter the employee’s Street Address, City, State, and Zip Code
Next select the Save button
Repeat steps 2a i-v until all dismissed employees have been added, then select Continue
Continue if you have no dismissed employees for this year
In the Add your previous payrolls section, select the Add previous payroll button
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
Then select a Pay period start date and Pay period end date
Next, select Save and Continue
Then for the first employee, select the Add amounts link
Next, specify the Regular wage and Regular hours worked
If needed, select the Add bonuses, tips or commissions link to add additional details
For deductions and contributions, this will need to be amended manually after you’ve submitted your historical payroll at the end of these steps
Then select the Calculate tax amounts link, taxes will automatically be calculated and populated in the fields for you
Review the tax calculations and correct any amounts that differ from tax payments that have already been made, then select Save
Repeat step 3d i-v for each employee listed
Earnings and taxes will now be updated with the correct Gross pay, select Save and continue
Repeat step 6 as needed for each payroll run this year until all are recorded in your list of this year’s payrolls
Then select the Review tax liabilities button
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
Then select Submit
Next, select Finish
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
Run a regular payroll based on your business’ pay schedule. The deadline to submit payroll runs is 4 business days prior to payout, by6:30 pm ET on business days. Use the below steps to run a payroll:
Select the Payroll section
Next, select the Pay… button and then select Employees
In the Pay Period section, choose an available period in the dropdown
Then select Continue
In the Hours and Earnings section, review your employees’ information
If needed, select an employee to edit their Hours, Additional Earnings, Reimbursements, and Payment Method, then select Confirm
Next, select Save and Continue
In the Review and Submit section, review the Business Pays and Debits, as well as Employee Take Home sections as needed
Select Submit Payroll to start processing your payroll, and your payroll run will appear in the Payroll History list.
When the payroll run is successfully marked as Processed, your employees will receive their direct deposit payments and their pay stubs by email. To cancel a payroll run while it’s still in the Submitted status or download pay stubs as PDFs, go to Review Payroll Runs and Contractor Payments below.
Check Payments
If you’re importing expenses via via Bank Connections or Bank Reconciliation and you’ve paid employees using check payments, the automatically created expense for the check payment can be addressed in one of two ways:
If not using Bank Rec - All employee check payment expenses should be deleted to avoid duplicate expenses
The deadline to submit payments for your contractors is 4 business days prior to payout, by6:30 pm ET on business days. To pay your contractors, use the below steps:
Select the Payroll section
Next, select the Pay… button and then select Contractors
In the Pay Date section, choose the Pay Date
Then select Continue
In the Hours and Payment section, select a contractor
Contractors’ pay total are automatically set to $0, edit the Hours field, and if needed, the Bonus and Reimbursement fields
Next, for Payment Method, select Check or Direct Deposit
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
Then select Confirm
Next, select Continue
In the Review and Submit section, review the Total Amount details and the Business Pays section as needed
Select Submit Payment to start processing your payments, and your contractor payment will appear in the Payment History list.
Your contractor payment will be submitted today, and updated to Processed status once received by Gusto. If you need to cancel a contractor payment while it’s still in the Submitted status, or download contractor payment receipts, go to Review Payroll Runs and Contractor Payments below.
Share Contractor Payment Receipts
Payment receipts will be generated on the pay date selected. To share the payment receipt with your contractors, use the below steps to download a PDF for each contractor:
Select the Payroll section
Under Payment History, select the contractor payment
Under Business Pays on the Pay Date, select a contractor
The contractor’s payment receipt will be displayed, use your browser’s print dialog to download it as a PDF
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
While viewing a payroll run pay period, you can select either:
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
While viewing a contractor payment pay period, you can select either:
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
When can I cancel a payroll run or contractor payment?
The option to cancel a payroll run or a payment is only available while the payroll or payment is in Submitted status. While in the Submitted status, payroll runs or payments must be canceled before the deadline of 6:30 pm ET 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 do I record previous payments to 1099 Contractors?
Previous payments made to 1099 contractors before you onboard to FreshBooks Payroll can be manually added in by our Support team. Use the below steps:
Add any contractors who have been paid this year in your Team Members
Once all previously paid contractors have been added, reach out to our Support team directly
In your ticket to Support, specify each contractor’s name, the amount, and the payment date for each payment made this year.
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.
All off-cycle payroll runs, including wage corrections and reconciliation payrolls can only be viewed in the Payroll Journal Report.
What happens to my expenses if I have FreshBooks Payroll powered by Gusto connected and an active bank connection?
Bank accounts used for payroll runs that are also connected via Bank Connections or Bank Reconciliation will handle payroll-related expenses differently. Depending on the payment method you’ve selected for your employees, the following will occur:
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
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.