diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9c5ca78c2f..3d9df9519c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -37,6 +37,7 @@ We use *breaking :warning:* to mark changes that are not backward compatible (re
 - [#5641](https://github.com/thanos-io/thanos/pull/5641) Query: Inject unshardable le label in query analyzer.
 - [#5685](https://github.com/thanos-io/thanos/pull/5685) Receive: Make active/head series limiting configuration per tenant by adding it to new limiting config.
 - [#5411](https://github.com/thanos-io/thanos/pull/5411) Tracing: Change Jaeger exporter from OpenTracing to OpenTelemetry. *Options `RPC Metrics`, `Gen128Bit` and `Disabled` are now deprecated and won't have any effect when set :warning:.*
+- [#5766](https://github.com/thanos-io/thanos/pull/5766) Compact: Apply retention before compaction.
 
 ### Removed
 
diff --git a/cmd/thanos/compact.go b/cmd/thanos/compact.go
index 166aa5d7c9..6c910f8f79 100644
--- a/cmd/thanos/compact.go
+++ b/cmd/thanos/compact.go
@@ -420,6 +420,15 @@ func runCompact(
 	}
 
 	compactMainFn := func() error {
+		// TODO(bwplotka): Find a way to avoid syncing if no op was done.
+		if err := sy.SyncMetas(ctx); err != nil {
+			return errors.Wrap(err, "sync before retention")
+		}
+
+		if err := compact.ApplyRetentionPolicyByResolution(ctx, logger, bkt, sy.Metas(), retentionByResolution, compactMetrics.blocksMarked.WithLabelValues(metadata.DeletionMarkFilename, "")); err != nil {
+			return errors.Wrap(err, "retention failed")
+		}
+
 		if err := compactor.Compact(ctx); err != nil {
 			return errors.Wrap(err, "compaction")
 		}
@@ -454,15 +463,6 @@ func runCompact(
 			level.Info(logger).Log("msg", "downsampling was explicitly disabled")
 		}
 
-		// TODO(bwplotka): Find a way to avoid syncing if no op was done.
-		if err := sy.SyncMetas(ctx); err != nil {
-			return errors.Wrap(err, "sync before retention")
-		}
-
-		if err := compact.ApplyRetentionPolicyByResolution(ctx, logger, bkt, sy.Metas(), retentionByResolution, compactMetrics.blocksMarked.WithLabelValues(metadata.DeletionMarkFilename, "")); err != nil {
-			return errors.Wrap(err, "retention failed")
-		}
-
 		return cleanPartialMarked()
 	}