diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2b21adc101..44721110d4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -22,6 +22,7 @@ We use *breaking :warning:* to mark changes that are not backward compatible (re
 - [#5206](https://github.com/thanos-io/thanos/pull/5206) Cache: add timeout for groupcache's fetch operation.
 - [#5218](https://github.com/thanos-io/thanos/pull/5218) Tools: Run bucket downsample tools continuously.
 - [#5224](https://github.com/thanos-io/thanos/pull/5224) Receive: Remove sort on label hashing
+- [#5231](https://github.com/thanos-io/thanos/pull/5231) Tools: Bucket verify tool ignores blocks with deletion markers.
 
 ### Removed
 
diff --git a/cmd/thanos/tools_bucket.go b/cmd/thanos/tools_bucket.go
index 6964b4c71b..959d2a146c 100644
--- a/cmd/thanos/tools_bucket.go
+++ b/cmd/thanos/tools_bucket.go
@@ -333,7 +333,9 @@ func registerBucketVerify(app extkingpin.AppClause, objStoreConfig *extflag.Path
 			return err
 		}
 
-		fetcher, err := block.NewMetaFetcher(logger, block.FetcherConcurrency, bkt, "", extprom.WrapRegistererWithPrefix(extpromPrefix, reg), nil)
+		// We ignore any block that has the deletion marker file.
+		filters := []block.MetadataFilter{block.NewIgnoreDeletionMarkFilter(logger, bkt, 0, block.FetcherConcurrency)}
+		fetcher, err := block.NewMetaFetcher(logger, block.FetcherConcurrency, bkt, "", extprom.WrapRegistererWithPrefix(extpromPrefix, reg), filters)
 		if err != nil {
 			return err
 		}