diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7ec7a02889..88a9e98fb0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -24,8 +24,10 @@ We use *breaking :warning:* to mark changes that are not backward compatible (re
 - [#3378](https://github.com/thanos-io/thanos/pull/3378) Ruler: added the ability to send queries via the HTTP method POST. Helps when alerting/recording rules are extra long because it encodes the actual parameters inside of the body instead of the URI. Thanos Ruler now uses POST by default unless `--query.http-method` is set `GET`.
 - [#3381](https://github.com/thanos-io/thanos/pull/3381) Querier UI: Add ability to enable or disable metric autocomplete functionality.
 - [#2979](https://github.com/thanos-io/thanos/pull/2979) Replicator: Add the ability to replicate blocks within a time frame by passing --min-time and --max-time
+- [#3409](https://github.com/thanos-io/thanos/pull/3409) Compactor: Added support for no-compact-mark.json which excludes the block from compaction.
 
 ### Fixed
+
 - [#3257](https://github.com/thanos-io/thanos/pull/3257) Ruler: Prevent Ruler from crashing when using default DNS to lookup hosts that results in "No such hosts" errors.
 - [#3331](https://github.com/thanos-io/thanos/pull/3331) Disable Azure blob exception logging
 - [#3341](https://github.com/thanos-io/thanos/pull/3341) Disable Azure blob syslog exception logging
@@ -33,6 +35,9 @@ We use *breaking :warning:* to mark changes that are not backward compatible (re
 
 ### Changed
 
+- [#3410](https://github.com/thanos-io/thanos/pull/3410) Compactor: Changed metric `thanos_compactor_blocks_marked_for_deletion_total` to `thanos_compactor_blocks_marked_total` with `marker` label.
+    Compactor will now automatically disable compaction for blocks with large index that would output blocks after compaction larger than specified value (by default: 64GB). This automatically
+    handles the Promethus [format limit](https://github.com/thanos-io/thanos/issues/1424).
 - [#2906](https://github.com/thanos-io/thanos/pull/2906) Tools: Refactor Bucket replicate execution. Removed all `thanos_replicate_origin_.*` metrics.
     - `thanos_replicate_origin_meta_loads_total` can be replaced by `blocks_meta_synced{state="loaded"}`.
     - `thanos_replicate_origin_partial_meta_reads_total` can be replaced by `blocks_meta_synced{state="failed"}`.
diff --git a/cmd/thanos/compact.go b/cmd/thanos/compact.go
index 9b7ab67086..5d0ab85794 100644
--- a/cmd/thanos/compact.go
+++ b/cmd/thanos/compact.go
@@ -125,10 +125,13 @@ func runCompact(
 		Name: "thanos_compactor_block_cleanup_failures_total",
 		Help: "Failures encountered while deleting blocks in compactor.",
 	})
-	blocksMarkedForDeletion := promauto.With(reg).NewCounter(prometheus.CounterOpts{
-		Name: "thanos_compactor_blocks_marked_for_deletion_total",
-		Help: "Total number of blocks marked for deletion in compactor.",
-	})
+	blocksMarked := promauto.With(reg).NewCounterVec(prometheus.CounterOpts{
+		Name: "thanos_compactor_blocks_marked_total",
+		Help: "Total number of blocks marked in compactor.",
+	}, []string{"marker"})
+	blocksMarked.WithLabelValues(metadata.NoCompactMarkFilename)
+	blocksMarked.WithLabelValues(metadata.DeletionMarkFilename)
+
 	garbageCollectedBlocks := promauto.With(reg).NewCounter(prometheus.CounterOpts{
 		Name: "thanos_compact_garbage_collected_blocks_total",
 		Help: "Total number of blocks marked for deletion by compactor.",
@@ -245,7 +248,7 @@ func runCompact(
 			cf,
 			duplicateBlocksFilter,
 			ignoreDeletionMarkFilter,
-			blocksMarkedForDeletion,
+			blocksMarked.WithLabelValues(metadata.DeletionMarkFilename),
 			garbageCollectedBlocks,
 			conf.blockSyncConcurrency)
 		if err != nil {
@@ -281,9 +284,31 @@ func runCompact(
 		return errors.Wrap(err, "clean working downsample directory")
 	}
 
-	grouper := compact.NewDefaultGrouper(logger, bkt, conf.acceptMalformedIndex, enableVerticalCompaction, reg, blocksMarkedForDeletion, garbageCollectedBlocks)
+	grouper := compact.NewDefaultGrouper(
+		logger,
+		bkt,
+		conf.acceptMalformedIndex,
+		enableVerticalCompaction,
+		reg,
+		blocksMarked.WithLabelValues(metadata.DeletionMarkFilename),
+		garbageCollectedBlocks,
+	)
 	blocksCleaner := compact.NewBlocksCleaner(logger, bkt, ignoreDeletionMarkFilter, deleteDelay, blocksCleaned, blockCleanupFailures)
-	compactor, err := compact.NewBucketCompactor(logger, sy, grouper, compact.NewPlanner(logger, levels, noCompactMarkerFilter), comp, compactDir, bkt, conf.compactionConcurrency)
+	compactor, err := compact.NewBucketCompactor(
+		logger,
+		sy,
+		grouper,
+		compact.WithLargeTotalIndexSizeFilter(
+			compact.NewPlanner(logger, levels, noCompactMarkerFilter),
+			bkt,
+			int64(conf.maxBlockIndexSize),
+			blocksMarked.WithLabelValues(metadata.NoCompactMarkFilename),
+		),
+		comp,
+		compactDir,
+		bkt,
+		conf.compactionConcurrency,
+	)
 	if err != nil {
 		cancel()
 		return errors.Wrap(err, "create bucket compactor")
@@ -374,7 +399,7 @@ func runCompact(
 			return errors.Wrap(err, "sync before first pass of downsampling")
 		}
 
-		if err := compact.ApplyRetentionPolicyByResolution(ctx, logger, bkt, sy.Metas(), retentionByResolution, blocksMarkedForDeletion); err != nil {
+		if err := compact.ApplyRetentionPolicyByResolution(ctx, logger, bkt, sy.Metas(), retentionByResolution, blocksMarked.WithLabelValues(metadata.DeletionMarkFilename)); err != nil {
 			return errors.Wrap(err, "retention failed")
 		}