diff --git a/cmd/cc-backend/main.go b/cmd/cc-backend/main.go
index 2db9a9f2..d515332f 100644
--- a/cmd/cc-backend/main.go
+++ b/cmd/cc-backend/main.go
@@ -589,6 +589,11 @@ func run() error {
 			cleanupDir = metricstore.Keys.Cleanup.RootDir
 		}
 
+		// Wire the job repository as NodeProvider so cleanup skips hosts
+		// with running jobs (same injection as runServer).
+		metricstore.InitMetrics(metricstore.BuildMetricList())
+		metricstore.GetMemoryStore().SetNodeProvider(repository.GetJobRepository())
+
 		cclog.Infof("Cleaning up checkpoints older than %s...", from.Format(time.RFC3339))
 		n, err := metricstore.CleanupCheckpoints(
 			metricstore.Keys.Checkpoints.RootDir, cleanupDir, from.Unix(), deleteMode)
diff --git a/pkg/metricstore/metricstore.go b/pkg/metricstore/metricstore.go
index c59b67e5..c763a903 100644
--- a/pkg/metricstore/metricstore.go
+++ b/pkg/metricstore/metricstore.go
@@ -251,9 +251,11 @@ func (ms *MemoryStore) GetMetricFrequency(metricName string) (int64, error) {
 }
 
 // SetNodeProvider sets the NodeProvider implementation for the MemoryStore.
-// This must be called during initialization to provide job state information
-// for selective buffer retention during Free operations.
-// If not set, the Free function will fall back to freeing all buffers.
+// The provider supplies the set of nodes in use by running jobs, which is
+// consulted by Free (selective buffer retention), FromCheckpoint (full-history
+// loading for used hosts), and CleanupCheckpoints (skipping used hosts).
+// It must be set before Init(): the checkpoint load inside Init reads it.
+// If not set, all three fall back to their provider-less behavior.
 func (ms *MemoryStore) SetNodeProvider(provider NodeProvider) {
 	ms.nodeProvider = provider
 }