diff --git a/cmd/db_cleanup.go b/cmd/db_cleanup.go
index 4a1b0535..be246915 100644
--- a/cmd/db_cleanup.go
+++ b/cmd/db_cleanup.go
@@ -59,6 +59,8 @@ func aptlyDbCleanup(cmd *commander.Command, args []string) error {
 		return err
 	}
 
+	context.CollectionFactory().Flush()
+
 	if verbose {
 		context.Progress().ColoredPrintf("@{y}Loading local repos:@|")
 	}
@@ -90,6 +92,8 @@ func aptlyDbCleanup(cmd *commander.Command, args []string) error {
 		return err
 	}
 
+	context.CollectionFactory().Flush()
+
 	if verbose {
 		context.Progress().ColoredPrintf("@{y}Loading snapshots:@|")
 	}
@@ -118,6 +122,8 @@ func aptlyDbCleanup(cmd *commander.Command, args []string) error {
 		return err
 	}
 
+	context.CollectionFactory().Flush()
+
 	if verbose {
 		context.Progress().ColoredPrintf("@{y}Loading published repositories:@|")
 	}
@@ -150,6 +156,8 @@ func aptlyDbCleanup(cmd *commander.Command, args []string) error {
 		return err
 	}
 
+	context.CollectionFactory().Flush()
+
 	// ... and compare it to the list of all packages
 	context.Progress().ColoredPrintf("@{w!}Loading list of all packages...@|")
 	allPackageRefs := context.CollectionFactory().PackageCollection().AllPackageRefs()
@@ -192,6 +200,8 @@ func aptlyDbCleanup(cmd *commander.Command, args []string) error {
 		}
 	}
 
+	context.CollectionFactory().Flush()
+
 	// now, build a list of files that should be present in Repository (package pool)
 	context.Progress().ColoredPrintf("@{w!}Building list of files referenced by packages...@|")
 	referencedFiles := make([]string, 0, existingPackageRefs.Len())