diff --git a/reframe/core/pipeline.py b/reframe/core/pipeline.py
index 34f12cda8a..0f7279ca13 100644
--- a/reframe/core/pipeline.py
+++ b/reframe/core/pipeline.py
@@ -802,10 +802,11 @@ def _setup_paths(self):
         """Setup the check's dynamic paths."""
         self.logger.debug('setting up paths')
         try:
-            self._stagedir = rt.runtime().resources.make_stagedir(
+            resources = rt.runtime().resources
+            self._stagedir = resources.make_stagedir(
                 self.current_system.name, self._current_partition.name,
                 self._current_environ.name, self.name)
-            self._outputdir = rt.runtime().resources.make_outputdir(
+            self._outputdir = resources.make_outputdir(
                 self.current_system.name, self._current_partition.name,
                 self._current_environ.name, self.name)
         except OSError as e:
diff --git a/reframe/core/runtime.py b/reframe/core/runtime.py
index 64576b519a..13406bbd70 100644
--- a/reframe/core/runtime.py
+++ b/reframe/core/runtime.py
@@ -113,9 +113,18 @@ def _makedir(self, *dirs, wipeout=False):
         os.makedirs(ret, exist_ok=True)
         return ret
 
-    def _run_suffix(self):
+    def _format_dirs(self, *dirs):
+        try:
+            last = dirs[-1]
+        except IndexError:
+            return dirs
+
         current_run = runtime().current_run
-        return '_%s' % current_run if current_run > 0 else ''
+        if current_run == 0:
+            return dirs
+
+        last += '_retry%s' % current_run
+        return (*dirs[:-1], last)
 
     @property
     def timestamp(self):
@@ -125,21 +134,17 @@ def timestamp(self):
     def output_prefix(self):
         """The output prefix directory of ReFrame."""
         if self.outputdir is None:
-            return os.path.join(self.prefix, 'output' + self._run_suffix(),
-                                self.timestamp)
+            return os.path.join(self.prefix, 'output', self.timestamp)
         else:
-            return os.path.join(self.outputdir + self._run_suffix(),
-                                self.timestamp)
+            return os.path.join(self.outputdir, self.timestamp)
 
     @property
     def stage_prefix(self):
         """The stage prefix directory of ReFrame."""
         if self.stagedir is None:
-            return os.path.join(self.prefix, 'stage' + self._run_suffix(),
-                                self.timestamp)
+            return os.path.join(self.prefix, 'stage', self.timestamp)
         else:
-            return os.path.join(self.stagedir + self._run_suffix(),
-                                self.timestamp)
+            return os.path.join(self.stagedir, self.timestamp)
 
     @property
     def perflog_prefix(self):
@@ -149,10 +154,12 @@ def perflog_prefix(self):
             return self.perflogdir
 
     def make_stagedir(self, *dirs, wipeout=True):
-        return self._makedir(self.stage_prefix, *dirs, wipeout=wipeout)
+        return self._makedir(self.stage_prefix,
+                             *self._format_dirs(*dirs), wipeout=wipeout)
 
     def make_outputdir(self, *dirs, wipeout=True):
-        return self._makedir(self.output_prefix, *dirs, wipeout=wipeout)
+        return self._makedir(self.output_prefix,
+                             *self._format_dirs(*dirs), wipeout=wipeout)
 
 
 class RuntimeContext: