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How to Integrate with Paychex Flex
How to Integrate with Paychex Flex

Step by step instructions on how to integrate with Paychex Flex

Rachel avatar
Written by Rachel
Updated this week

Overview: The integration with Paychex Flex is done through an export/import process. When it's time to process payroll, you will export the Paychex Flex-specific file and upload it into their system.


Enable the Paychex Flex Integration

1. To enable the Paychex Flex integration, start by going to Settings --> Integrations:

2. Click the Paychex Settings button:

3. Check the box next to Enable Integration with Paychex and enter your:

  • Paychex Client ID—The 8 alphanumeric Client ID can be found in your Paychex Flex account under the account name:

  • Paychex Pay Codes/Components—Pay Components/Codes are the standard descriptions you set in Paychex such as Hourly, Overtime, PTO, etc.

Click Save once done:

Note: The additional mapping categories outside of Reg, OT, and DBT are controlled by your Time Off Types, which can be found by going to Settings --> Time Off in Buddy Punch.

Enter Employee IDs

Any worker you want to show up on the Paychex Flex export needs to have an Employee ID. This ID should match what is found in the Paychex Flex system under People:

More details on where to find/enter the Employee ID in Buddy Punch can be found here:

Export the Paychex Flex File

1. To export the Paychex Flex file, go to Reports --> Payroll Export:

2. Choose your pay period and any filters, and click Run Report. You'll then want to click the Export dropdown followed by Paychex Flex 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.

As a final step, you can now import your data into Paychex Flex. We recommend contacting your Paychex Flex representative if you have questions about this step.


Q: Are contractors supported?

A: No, contractors are not supported.

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