diff --git a/server/server.go b/server/server.go
index dce01f4b..17a55b47 100644
--- a/server/server.go
+++ b/server/server.go
@@ -150,12 +150,14 @@ func New(cfg Config) (*Server, error) {
 
 	// Setup HTTP server
 	router := mux.NewRouter()
-	if cfg.RegisterInstrumentation {
-		RegisterInstrumentation(router)
-	}
 	if cfg.PathPrefix != "" {
+		// Expect metrics and pprof handlers to be prefixed with server's path prefix.
+		// e.g. /loki/metrics or /loki/debug/pprof
 		router = router.PathPrefix(cfg.PathPrefix).Subrouter()
 	}
+	if cfg.RegisterInstrumentation {
+		RegisterInstrumentation(router)
+	}
 	httpMiddleware := []middleware.Interface{
 		middleware.Tracer{
 			RouteMatcher: router,