ArcGIS Server federation fails with "User not allowed for this account" after reinstall

Error Message

Attempting to federate ArcGIS Server with Portal for ArcGIS returns the following error message:

Failed to federate ArcGIS Server site 'https://<arcgisserver.domain.com>:6443/arcgis' with Portal for ArcGIS.
Failed to update security configuration for ArcGIS Server 'https://<arcgisserver.domain.com>:6443/arcgis'. The
server at 'https://<arcgisserver.domain.com>:6443/arcgis/admin/security/config/update’ returned an error.
Failed to update the security configuration. Cannot update security configuration to federate with Portal as
server is not registered with Portal. Server machine returned an error. 'User not allowed for this account'.

This occurs after uninstalling and reinstalling ArcGIS Server and Portal for ArcGIS on the same machine and attempting to federate again.

Cause

Residual files and configuration data from previous ArcGIS Enterprise installations remain on the machine after uninstall.

These may include:

• Configuration store directories, for example, C:\arcgisserver, C:\arcgisportal.
• Security keys and tokens.
• Machine identity and previous federation references.

This leads to inconsistencies in the ArcGIS Server security configuration, causing federation to fail with authorization errors.

Solution or Workaround

1. Uninstall all ArcGIS Enterprise components:
   • ArcGIS Server
   • Portal for ArcGIS
   • ArcGIS Data Store (if applicable)
2. Manually delete residual directories:
   • C:\arcgisserver
   • C:\arcgisportal
3. Verify that no ArcGIS-related services remain.
4. Restart the machine.
5. Reinstall ArcGIS Enterprise components.
6. Create a new ArcGIS Server site (do not reuse existing configuration stores).
7. Federate ArcGIS Server with Portal for ArcGIS.

Alternative

Deploy the ArcGIS Enterprise components on a clean virtual machine to ensure no residual configuration data is present.