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How To Set Up & Download Payroll File For Paychex Flex
How To Set Up & Download Payroll File For Paychex Flex
Christina Kao avatar
Written by Christina Kao
Updated over 6 months ago

Workyard offers you the ability to export your time data for team members to Paychex Flex. Making payroll a breeze!

How It Works

If you want to use Workyard's integrations, the first step is to contact us to let us know that you would like to use the Paychex Flex integration. Our team will configure your account to produce the appropriate Paychex Flex file format to ensure a successful integration. After your account has been configured, you can proceed with the following steps to complete the process.

Exporting Your Payroll File

Step 1: Navigate to the Timecards and click on Export

Step 2: Select the Date range, Team members, and Integration, and then click "Start Export"

Step 3: A new page called the Workyard File Exporter will open. From here, you'll be asked to enter the Paychex Flex Employee ID in the Target ID column. Once completed, click on "Save Changes".


Step 4: Enter the pay item codes from Paychex Flex for Regular, Overtime, or Double time.

Step 5: Once you've completed all your mappings, click the Download File button in the top right-hand corner.

Step 6: Save the Time Card File download from Workyard to your computer; from here, you'll need to import that file into Paychex Flex.

Importing Your Payroll File

Now that you've gotten your Paychex Flex specific report downloaded, you'll want to import it into the Paychex Flex system. To do this:

  • 1) Click the Payroll Center

  • 2) Click on More Options

  • 3) Click the Browse Files button

  • Select the export file you created in Workyard, followed by Open.

  • File information will display in the Import Pay Period panel on the right. From the Start Payroll panel, select Submit Payroll.

  • Lastly, click Process to import the file.

If you run into this error (below) you'll need to contact your Paychex support team to enable file importing. (Paychex Help Article: here)


Our customer support team is always here to help if you have questions or would like some help. Contact us at help@workyard.com or message us via the Help icon.

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