diff --git a/x-pack/elastic-agent/pkg/agent/cmd/enroll_cmd.go b/x-pack/elastic-agent/pkg/agent/cmd/enroll_cmd.go
index 5750e2ce4b0..25365c9afe9 100644
--- a/x-pack/elastic-agent/pkg/agent/cmd/enroll_cmd.go
+++ b/x-pack/elastic-agent/pkg/agent/cmd/enroll_cmd.go
@@ -407,7 +407,9 @@ func (c *enrollCmd) prepareFleetTLS() error {
 	}
 
 	if c.options.FleetServer.InternalPort > 0 {
-		c.log.Debugf("Internal endpoint configured to: %d. Changing this value is not supported.", c.options.FleetServer.InternalPort)
+		if c.options.FleetServer.InternalPort != defaultFleetServerInternalPort {
+			c.log.Warnf("Internal endpoint configured to: %d. Changing this value is not supported.", c.options.FleetServer.InternalPort)
+		}
 		c.options.InternalURL = fmt.Sprintf("%s:%d", defaultFleetServerInternalHost, c.options.FleetServer.InternalPort)
 	}