diff --git a/pkgs/by-name/pr/prometheus/package.nix b/pkgs/by-name/pr/prometheus/package.nix
index 40cfe2fec8f0..7ab27fa8cefa 100644
--- a/pkgs/by-name/pr/prometheus/package.nix
+++ b/pkgs/by-name/pr/prometheus/package.nix
@@ -198,6 +198,10 @@ buildGoModule (finalAttrs: {
   checkFlags = [
     # Skip for issue during TSDB compaction
     "-skip=TestBlockRanges"
+    # both are flaky and might fail when the builder is under load
+    # https://github.com/prometheus/prometheus/issues/16450
+    "-skip=TestDelayedCompaction"
+    "-skip=TestHeadCompactionWhileScraping"
   ]
   ++ lib.optionals stdenv.hostPlatform.isAarch64 [
     "-skip=TestEvaluations/testdata/aggregators.test"