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Paychex Flex Configuration

B
Brian Zurawski
22 Oct, 2026 - Updated 19 days ago
Payroll Integrations

Paychex Flex Configuration

Configure the Paychex Flex payroll export.

Follow these steps to enable and configure the Paychex Flex payroll integration.

Plan required: Payroll integrations are an advanced TimeTrakGO feature, available on the PLUS plan or higher. Free setup and configuration assistance is available from our customer care team.

Step 1 Turn On the Payroll Integrations Feature

  1. Go to Feature Manager.
  2. Under System Options, find the Payroll Integrations card and turn on the toggle.
Payroll Integrations card under System Options in Feature Manager with the toggle off

The Integrations - Activation Question window asks if you want to enable the Pass to Payroll options for all users. Yes is recommended. If certain employees should not be sent to payroll, such as temporary employees paid through a temp agency or salaried employees, you can change this for each user in the Users area at any time.

Integrations Activation Question asking to enable Pass to Payroll for all users

Step 2 Open the Payroll Interfaces Page

Click Settings on the Payroll Integrations card. This opens the Payroll Interfaces page, which lists every available payroll integration.

Settings button on the Payroll Integrations card

Step 3 Turn On the Paychex Flex Integration

Find the PayChex card and turn on its toggle. Then click Settings on that card to open the Paychex Flex Export page.

Payroll Interfaces page with the PayChex toggle highlighted

Step 4 Configure Settings

On the Settings tab: Enter your Paychex Company ID, then set the Export File Name. The file is saved as a .csv.

The Contact Customer Care panel lists phone, email, and live chat options if you want help with setup.

Paychex Flex Export Settings tab

Step 5 Map Pay Codes

On the Pay Codes tab, enter the Paychex Flex Pay Component for each TimeTrakGO Pay Code. To leave a pay code out of the export, turn off its Pass to Payroll toggle.

Paychex Flex Export Pay Codes tab with the Paychex Flex Pay Component column

Step 6 Export Hours to Paychex

You are now ready to export hours to Paychex. Once configured, the export file is available from the TimeTrakGO Dashboard, in the Employee Hours section. Click Export Options, then choose Paychex Flex. This downloads a file you can upload into Paychex.

Exporting hours to Paychex

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