Exact Online and Paychex integration

What moves between them

Worker records and pay period data flow from Paychex into Exact Online. Paychex worker records are synced into Exact Online employees, and payroll data such as pay components and check records are mapped into Exact Online cost transactions and journal entries for accounting purposes. The integration polls Paychex on a schedule or receives webhook notifications for worker and payroll events, then queries the full entity data and writes the transformed records into Exact Online.

How ml-connector handles it

ml-connector stores both OAuth2 credential sets encrypted and handles the different token models: for Exact Online it manages the 10-minute access token and rotating 30-day refresh token, using the division ID from the /api/v1/current/Me endpoint; for Paychex it proactively refreshes the Client Credentials access token before expiry since no refresh token is issued. Paychex webhooks are notification-only, so ml-connector always fetches the full worker or payroll entity via GET after receiving a webhook. Exact Online webhook payloads include only the entity key and action, so ml-connector similarly fetches full entity data before writing. Workers are mapped to Exact Online employees, and pay period records are mapped to cost transactions using Exact Online cost centers. Both systems receive retries on transient failures, and every record is tracked in the audit log so replays are possible if a write fails.

A real-world example

A mid-market professional services firm runs Exact Online for accounting and project costing and uses Paychex for payroll and HR across multiple offices. Before the integration, the HR team manually added new hires to Exact Online after they were created in Paychex, and payroll registers had to be exported and re-entered to update labor cost allocations in Exact Online's cost transactions. With Paychex and Exact Online connected, new hires and terminations flow automatically from Paychex into Exact Online employees, and pay period data syncs to cost transactions mapped to the correct cost centers. Month-end close no longer requires manual reconciliation of employee headcount across the two systems.

What you can do

• •Sync Paychex workers into Exact Online employees so new hires and terminations are reflected automatically.
• •Map Paychex payroll data and pay components into Exact Online cost transactions and journal entries.
• •Authenticate Paychex with OAuth2 Client Credentials and Exact Online with OAuth2 Authorization Code Grant.
• •Poll Paychex and Exact Online on a schedule tied to your payroll calendar, with automatic retries and full audit trails.
• •Fetch full entity data after webhook notifications from either system so all required fields are captured.

Questions

Which direction does data flow between Exact Online and Paychex?

The main flow is from Paychex into Exact Online. Worker records and payroll data move from Paychex into Exact Online employees and cost transactions. Exact Online is the accounting source of truth and does not write data back to Paychex.

How does ml-connector handle the different token models between the two systems?

Exact Online issues 10-minute access tokens with rotating 30-day refresh tokens, which ml-connector manages automatically. Paychex does not issue refresh tokens, so ml-connector proactively acquires a new access token from the Client Credentials endpoint before expiry to avoid service interruption.

Do Paychex webhook payloads include all the payroll data needed?

No. Paychex webhooks are notification-only and contain only the entity key and action type. ml-connector always follows each webhook with a GET request to fetch the full worker or pay period record, ensuring all required fields are captured before writing to Exact Online.