diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4b961d65ea3..c0abb551fce 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -25,6 +25,7 @@ We use *breaking :warning:* to mark changes that are not backward compatible (re
 - [#7326](https://github.com/thanos-io/thanos/pull/7326) Query: fixing exemplars proxy when querying stores with multiple tenants.
 - [#7403](https://github.com/thanos-io/thanos/pull/7403) Sidecar: fix startup sequence
 - [#7484](https://github.com/thanos-io/thanos/pull/7484) Proxy: fix panic in lazy response set
+- [#7492](https://github.com/thanos-io/thanos/pull/7492) Compactor: update filtered blocks list before second downsample pass.
 
 ### Added
 
diff --git a/cmd/thanos/compact.go b/cmd/thanos/compact.go
index 43fecdebc1e..06d3ffaaa38 100644
--- a/cmd/thanos/compact.go
+++ b/cmd/thanos/compact.go
@@ -488,6 +488,14 @@ func runCompact(
 				return errors.Wrap(err, "sync before second pass of downsampling")
 			}
 
+			// Regenerate the filtered list of blocks after the sync,
+			// to include the blocks created by the first pass.
+			filteredMetas = sy.Metas()
+			noDownsampleBlocks = noDownsampleMarkerFilter.NoDownsampleMarkedBlocks()
+			for ul := range noDownsampleBlocks {
+				delete(filteredMetas, ul)
+			}
+
 			if err := downsampleBucket(
 				ctx,
 				logger,
diff --git a/test/e2e/compact_test.go b/test/e2e/compact_test.go
index eb0ceb00544..54c04fe91af 100644
--- a/test/e2e/compact_test.go
+++ b/test/e2e/compact_test.go
@@ -766,7 +766,7 @@ func testCompactWithStoreGateway(t *testing.T, penaltyDedup bool) {
 		// NOTE: We cannot assert on intermediate `thanos_blocks_meta_` metrics as those are gauge and change dynamically due to many
 		// compaction groups. Wait for at least first compaction iteration (next is in 5m).
 		testutil.Ok(t, c.WaitSumMetricsWithOptions(e2emon.Greater(0), []string{"thanos_compact_iterations_total"}, e2emon.WaitMissingMetrics()))
-		testutil.Ok(t, c.WaitSumMetricsWithOptions(e2emon.Equals(19), []string{"thanos_compact_blocks_cleaned_total"}, e2emon.WaitMissingMetrics()))
+		testutil.Ok(t, c.WaitSumMetricsWithOptions(e2emon.Equals(18), []string{"thanos_compact_blocks_cleaned_total"}, e2emon.WaitMissingMetrics()))
 		testutil.Ok(t, c.WaitSumMetricsWithOptions(e2emon.Equals(0), []string{"thanos_compact_block_cleanup_failures_total"}, e2emon.WaitMissingMetrics()))
 		testutil.Ok(t, c.WaitSumMetricsWithOptions(e2emon.Equals(0), []string{"thanos_compact_aborted_partial_uploads_deletion_attempts_total"}, e2emon.WaitMissingMetrics()))
 		testutil.Ok(t, c.WaitSumMetricsWithOptions(e2emon.Equals(0), []string{"thanos_compact_group_compactions_total"}, e2emon.WaitMissingMetrics()))
@@ -775,7 +775,7 @@ func testCompactWithStoreGateway(t *testing.T, penaltyDedup bool) {
 		testutil.Ok(t, c.WaitSumMetricsWithOptions(e2emon.Equals(7), []string{"thanos_compact_group_compaction_runs_started_total"}, e2emon.WaitMissingMetrics()))
 		testutil.Ok(t, c.WaitSumMetricsWithOptions(e2emon.Equals(7), []string{"thanos_compact_group_compaction_runs_completed_total"}, e2emon.WaitMissingMetrics()))
 
-		testutil.Ok(t, c.WaitSumMetricsWithOptions(e2emon.Equals(2), []string{"thanos_compact_downsample_total"}, e2emon.WaitMissingMetrics()))
+		testutil.Ok(t, c.WaitSumMetricsWithOptions(e2emon.Equals(0), []string{"thanos_compact_downsample_total"}, e2emon.WaitMissingMetrics()))
 		testutil.Ok(t, c.WaitSumMetricsWithOptions(e2emon.Equals(0), []string{"thanos_compact_downsample_failures_total"}, e2emon.WaitMissingMetrics()))
 
 		testutil.Ok(t, str.WaitSumMetricsWithOptions(