diff --git a/scale_build/epoch.py b/scale_build/epoch.py
index 9a6f343..869b5e8 100644
--- a/scale_build/epoch.py
+++ b/scale_build/epoch.py
@@ -2,6 +2,7 @@ import logging
 import os
 
 from .clean import complete_cleanup
+from .preflight import setup_dirs
 from .utils.manifest import get_manifest
 from .utils.paths import TMP_DIR
 
@@ -25,5 +26,6 @@ def check_epoch():
                 logger.warning('Build epoch changed! Removing temporary files and forcing clean build.')
                 update_epoch(current_epoch)
                 complete_cleanup()
+                setup_dirs()
     else:
         update_epoch(current_epoch)