Connect Paychex Flex to Entra ID

ezOnboard connects through a Paychex Flex integrated app with its own API key and client secret. Use a Super Admin, Security Admin or custom role with Integrated Apps Administration to create it.

Create an app named ezOnboard. Under Access settings, turn on Company and worker APIs and choose Read only. Leave Payroll and check APIs off. Accept the Legal Notice and API License Agreement, then save.

Copy the API Key and Client Secret shown after saving. Store them securely and share them only with people who need access.

To include more companies, add each one under Company Access and turn on Access. You’ll need the API key and client secret in step 5.

The agent runs as a Windows service on your server with Windows Server 2019 or later. No domain join is required. It connects to Paychex Flex, ezOnboard and Microsoft Graph over outbound HTTPS. No inbound firewall rules are needed.

Download the signed MSI and enrollment bundle from the portal. Save the install code. The portal shows it only once. Run the MSI and enter the code. The agent uses a local virtual account by default, with no password to manage. The installer checks outbound access and the clock before making changes. Domain and LDAP checks show “not needed”.

Add a Microsoft 365 connection in the portal. Choose the Directory and Licenses capabilities, then continue to Microsoft. Sign in as a Global Administrator and grant consent. The portal shows which capabilities have access. You can grant missing permissions later.

ezOnboard uses application permissions, not an administrator account or password. Revoke consent in Entra ID to remove its access. Each tenant connects to one organization.

In the portal, add Paychex Flex as an HR source using the API key and client secret. Your credentials are encrypted with your organization’s key and sent to your agent. The agent reads Paychex Flex from your network. Nobody at ezOnboard can read the credentials.

Choose a field to match people across both systems, usually work email or employee ID. The agent checks Paychex Flex every five minutes and catches up on any missed changes.

Choose which Paychex Flex fields update each directory attribute. Start with the defaults below, add custom fields or combine values. For example, build a display name from first and last names, format a job title or look up an office address by site.

Blank Paychex Flex fields leave directory values unchanged unless you configure the mapping to clear them.

Rules define who gets an account, which administrative unit it belongs to, how it’s named and which groups it joins. They also control offboarding. Use Paychex Flex fields, such as department and site, to make those choices.

Our implementation team helps you write the rules. With approvals enabled, your team must approve each rule change before the agent uses it.

Run a dry run for your whole workforce. The agent matches Paychex Flex records to existing accounts by employee ID, then work email, and previews changes without applying them. If two accounts match one person, that action stops for review.

Review the planned changes and the rules behind them in the portal. Adjust your rules and repeat the dry run until the results match your expectations.

Turn off dry run to apply changes. If a run would disable or move more accounts than your safety limits allow, it stops and alerts your team before making changes. We review the first runs with you.

HR continues working in Paychex Flex. Your rules handle new accounts, updates and offboarding on schedule. Get alerts by email, in the portal or by webhook when a run stops, the HR feed stops updating or the agent stops reporting. An inactive feed never triggers offboarding.