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Paychex Flex Integration Overview
Paychex Flex Integration Overview

Step by step instructions on how to integrate with Paychex Flex

Rachel avatar
Written by Rachel
Updated over a week ago

Overview: The integration with Paychex Flex is done through an export/import process. When it comes time to run payroll, you simply export a Paychex Flex-specific report and upload it into their system for payroll processing.


Additional Resources:

Setting Up Paychex Flex

You’ll want to start off by obtaining your Paychex Client ID, Employee IDs, and Paychex Codes from within your Paychex account. Employee ID’s can be found by clicking on the Time & Attendance tab, and select Employees:

The Paychex Client ID can be found by selecting Company from the menu:

If you’re not sure where to find your Paychex Codes, reach out to a Paychex representative or your payroll provider to assist you.

1. Once you've obtained your Paychex Employee IDs, Client ID, and Paychex Codes, you'll want to enable the Paychex integration in Buddy Punch. Start by going to Settings --> Integrations:

2. On the integrations page, click the Paychex Settings button:

3. Here you'll want to check the box next to "Enable integration with Paychex," enter your Paychex Client ID as well as your Paychex Codes. Save once done.

4. As a final step, you’ll want to take your Employee ID numbers obtained from your Paychex system and add them to each employee profile within Buddy Punch. The Employee ID entered into Buddy Punch needs to match what is found in Paychex to ensure all information is associated with the correct employee:

Exporting Time from Buddy Punch

1. To export time from Buddy Punch, start by going to Reports in the top navigation followed by Payroll Export:

2. You'll then want to select which pay period and employees you want to run the report on. Click Run Report to populate the selected data. You'll then want to export the report by clicking Export followed by Paychex Format:

Important: When exporting the Paychex file do not open and resave the file using Excel. Excel will change the format of numbers. For example, a "001" would become a "1". You will want to use notepad to edit if needed.

Importing Time into Paychex Flex

1. 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:

  • Click the Payroll tab (1)

  • Select the Active pay date in the Payroll panel (2)

  • Click the Browse Files button. (3)

  • Select the export file you created in Buddy Punch 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.

Important. If you add new employees make sure to add their Employee ID’s to Buddy Punch so they’ll be included in the Paychex export.


Q: Time is being applied to the wrong employees in Paychex. What am I doing wrong?

A: If time is being applied to the wrong employee in Paychex, then there's likely an issue with their Employee ID not matching in both systems. Please confirm that the Employee ID in Buddy Punch and Paychex match prior to exporting.

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