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Connecting Paychex Flex

Connect Time Tracker to Paychex Flex, map payroll items and contractors, and sync hours to payroll

Applies to: Workforce · Premium

Time Tracker syncs directly with Paychex Flex. There's no file to export: once you're connected, approved hours go to Paychex payroll when you sync, and your Paychex employees and contractors come into Time Tracker.

Getting There

In the left menu, click Paychex > Connect to Paychex. The page has three tabs: Connect to Paychex, Payroll Item Mapping, and Employee/Vendor Mapping.

Setting Up Paychex

Work through the Paychex Setup checklist on the right: Enable Paychex, Connect to Paychex, Sync Queue Settings, Account Settings, and Sync with Paychex. When you're connected, the page shows "Time Tracker is now connected with:" and your Paychex company, and tells you to start syncing by clicking Sync at the top of the screen.

Paychex Connected Page

The Connect to Paychex tab once you're connected. Your company name appears under "Time Tracker is now connected with".

What Syncs

Time Tracker
Direction
Paychex
Workers
Both ways
Employees (hourly or salary rate)
Vendors
From Paychex
Contractors
Time entries
To Paychex
Payroll
Pay items
From Paychex
Hourly compensation

Payroll Item Mapping

On the Payroll Item Mapping tab, choose which Paychex pay item each worker's hours are paid as. Click a worker's name to expand their row and choose a Regular (R), Holiday (H), and Sick (S) item. Contractors aren't listed, because they sync to Paychex Flex as 1099-NEC contractors.

Paychex Payroll Item Mapping

Payroll Item Mapping for Paychex, with one worker expanded.

Employee/Vendor Mapping (Contractors)

If some of your workers are paid as contractors through a vendor, link them on the Employee/Vendor Mapping tab so their time syncs to Paychex under that vendor.

  1. Click a vendor in the Paychex Vendors list on the left. It turns green.
  2. Tick that vendor's workers in the Paychex Employees list on the right.
  3. Click the left arrow in the middle to move them under the vendor.
  4. To remove a worker from a vendor, tick them on the left side and click the right arrow.

Paychex Employee Vendor Mapping

Vendors on the left, employees on the right.

Syncing

Approve the pay period's time, then click Sync at the top of the screen. The Sync section of the left menu also has the Sync Queue, Sync Log, and Auto Sync. See "How Syncing Works: Sync Queue, Sync Log, and Auto Sync", and if a sync fails, "My Integration Isn't Syncing: Finding and Fixing a Failed Sync".