Paychex Payroll Export

Updated June 01, 2026 17:37

If 7shifts users are using 7punches for time-clocking, or have a POS integration that includes labor, 7shifts users can export worked hours in a Paychex-ready format.

7shifts automatically sends timesheets to Paychex Flex, saving time on payroll processing and minimizing mistakes. You can easily export your staff's hours as regular, overtime, or holiday hours, helping you make informed decisions for your team and operations every day.

Things To Know

Important: Managers and Assistant Managers must be assigned to all relevant departments for wages to be included in the export. For example, if a Manager is only assigned to Department A, the export will not include employee wages in Departments B and C.

Access to this feature may require an upgrade from the current plan.
Only Admins can close all timesheets, which is a mandatory step to send payroll data to the integration successfully.

7shifts automatically sends timesheets to Paychex Flex, saving time on payroll processing and minimizing mistakes. 7shifts users can export staff hours as regular, overtime, or holiday hours, helping 7shifts users make informed decisions for team operations every day.

Activating the Paychex Export

In the left navigation bar, head to Integrations.
Search and select Paychex, then click Next.
Enter the Company Code and click Connect.
Click on Complete Set Up to add the export to the account.
Alternatively, find these settings under Integrations > My Integrations > Paychex > Settings.
Under the Custom Export Codes'tab, set the optional codes for Regular, Overtime, Double Overtime, and Holiday hours:
Click on the Payroll Mapping'tab and choose whether to enable 'Split Hours by Role' and 'Export Wages.'

The Split Hours by Role feature splits Employee hours by role on the CSV file. If Employees work more than one role, hours split on the CSV file, and the wage codes for those roles apply from Paychex.

The Export Wages feature splits the hours and overrides the Paychex wage with the wage entered in the Employee 7shifts profile for each role. If wages are entered for each job code in Paychex, this feature can remain off.

Mapping Employees and Roles with Paychex

Important: 7shifts users can return to this screen to update or edit codes by going to Integrations > My Integrations > Paychex > Settings.

Tip: If assistance is needed locating the file numbers for employees in Paychex, contact a Paychex representative.

To match employees in 7shifts to employees in Paychex, 7shifts users must input Paychex File Numbers in 7shifts.

Under the 'Payroll Mapping' tab, click on 'Edit employee IDs' or 'Map Roles.'
Select the Employees tab and enter the corresponding Paychex file number for each Employee. Scroll down and click Save.
Select the Roles tab to enable and map Labor Override Codes (optional). Enter the corresponding Labor Override Codes for each Role in 7shifts. Click Save before changing locations:

Preparing your Export File

Note: For multi-Location users, closing the Timesheet and exporting can occur on a Location basis. Select the correct Location in the 'Location' dropdown before selecting the 'Export' option.

Tip: Contact a Paychex representative for questions regarding importing the payroll data file into Paychex.

Before running the Paychex payroll export, ensure all punches are approved and the timesheet is closed.

In the left navigation bar, select the Time Clocking tab and the appropriate Pay Period.
Review and click Approve or Edit on punches, or choose Approve All:
Multi-Location users can sort by Location and approve punches by Location:
Once all punches are approved, close the Timesheet by selecting Close Timesheet in the top right corner.
With the Timesheet closed, export the file by selecting Export then Paychex:
Import the payroll data file to Paychex.

The columns included in the Paychex export are:

Company ID
Worker ID
Org
Job Number
Pay Component
Rate
Rate Number
Hours
Units
Line Date
Amount
Check Seq Number
Override State
Override Local
Override Local Jurisdiction
Labor Override
Role
Check Template
Output Type
Net Pay
Check Number
FIT Amt
SS Amt
Medicare Amt
Fed Backup Withholding Amt
State Tax Jurisdiction
SIT Amount
SDI Amt
Fam Leave
Med Leave
SUI Amt
State Misc Amt
State Surcharge Amt
State WC Amt
State Backup Withholding Amt
State Allocation %
Local Tax Jurisdiction
Local Tax Name
Local Amt
Local Allocation %

Including Paid Time Off (PTO)

To include Employee Paid Time Off and Paid Sick Time hours within the report, enable these features under Company Settings. After enabling Paid Time Off or Sick Time Off, input custom codes for Paychex using the following steps:

Go to Integrations > My Integrations > Paychex and click on Settings.
Under the Custom Export Codes tab, scroll down and set the optional codes for Paid Time Off, Sick Paid Time Off, and Unpaid Time Off hours :
Click Save.

These fields are optional. If no custom code is provided, the default columns for Paid Time Off, Sick Paid Time, and Unpaid Time Off export as:

PTO
SPTO
UPTO

Including Tips

Note: Click here to learn more about syncing tip data to payroll. Review the information to verify if the POS or tip source is compatible with the payroll provider.

Accounts using a supported POS integration can send tip data to 7shifts. This information can be included with time-clocking data when processing payroll.

Troubleshooting Paychex Import Errors

7shifts users may encounter specific error codes (WEBIMPORT309, WEBIMPORT139, or WEBIMPORT326) when attempting to upload the 7shifts payroll export file into Paychex. These errors occur because configuration settings within the Paychex account are not active to receive the detailed data sent from 7shifts. To resolve these errors, contact Paychex support to ensure the Paychex account settings are