diff --git a/scripts/benchmark.ts b/scripts/benchmark.ts
index aaacb65d..f8daa0ad 100644
--- a/scripts/benchmark.ts
+++ b/scripts/benchmark.ts
@@ -92,6 +92,7 @@ try {
 
 const INCREMENTAL_RUNS = 3;
 const QUERY_RUNS = 5;
+const QUERY_WARMUP_RUNS = 3;
 const PROBE_FILE = path.join(root, 'src', 'domain', 'queries.ts');
 
 function median(arr) {
@@ -133,9 +134,14 @@ const buildStart = performance.now();
 const buildResult = await buildGraph(root, { engine, incremental: false });
 const buildTimeMs = performance.now() - buildStart;
 
-const queryStart = performance.now();
-fnDepsData('buildGraph', dbPath);
-const queryTimeMs = performance.now() - queryStart;
+// Warmed median of QUERY_RUNS samples with `noTests: true` to match the
+// methodology used by query-benchmark.ts and the per-target `queries.*Ms`
+// block below (which calls `benchQuery`, also warmed). Earlier versions of
+// this script measured a single cold call, which conflated steady-state
+// query latency with NAPI/rusqlite/OS-page-cache init costs (~65ms on
+// macOS) and inflated growth from test-fixture files pulled in by new
+// native extractors. See #1113 for the methodology rationale.
+const queryTimeMs = benchQuery(fnDepsData, 'buildGraph', dbPath, { depth: 3, noTests: true });
 
 const stats = statsData(dbPath);
 const totalFiles = stats.files.total;
@@ -191,6 +197,11 @@ const targets = workerTargets() || selectTargets();
 console.error(`    hub=${targets.hub}, leaf=${targets.leaf}`);
 
 function benchQuery(fn, ...args) {
+	// Warmup runs prime NAPI bindings, the rusqlite statement cache, and the
+	// OS page cache so the timed loop measures steady-state query latency
+	// rather than first-call init (~65ms on macOS). Each call site warms
+	// independently — methodology does not rely on call ordering elsewhere.
+	for (let i = 0; i < QUERY_WARMUP_RUNS; i++) fn(...args);
 	const timings = [];
 	for (let i = 0; i < QUERY_RUNS; i++) {
 		const start = performance.now();
diff --git a/tests/benchmarks/regression-guard.test.ts b/tests/benchmarks/regression-guard.test.ts
index 1694c0d5..54b3f5ae 100644
--- a/tests/benchmarks/regression-guard.test.ts
+++ b/tests/benchmarks/regression-guard.test.ts
@@ -176,16 +176,19 @@ const SKIP_VERSIONS = new Set(['3.8.0']);
  *   absolute delta 10.4ms exactly at the MIN_ABSOLUTE_DELTA floor. Exempt
  *   this release; remove once 3.11.0+ data confirms stabilization.
  *
- * - 3.10.0:Query time — cumulative effect of adding two native extractors
- *   (Solidity #1100 + R #1102) in quick succession. Neither tripped the
- *   threshold individually (Solidity PR's Query time stayed at 49ms, R PR
- *   showed no warning), but the combined +110% (49.6 → ~105ms) on the
- *   `fnDepsData('buildGraph', dbPath)` measurement reflects natural graph
- *   growth: ~1100 LoC of new extractor code + 9 fixture files added to the
- *   self-build benchmark expand `buildGraph`'s transitive callee count and
- *   DB row counts. Tracked in #1113 — exempt this release; remove once
- *   3.11.0+ data captures the new steady-state and the per-language
- *   fixture footprint has been evaluated.
+ * - 3.10.0:Query time — methodology artifact, not a real regression. The
+ *   metric was a single-shot cold call to `fnDepsData('buildGraph', dbPath)`
+ *   with no warmup, no median, and `noTests: false` — so it captured ~65ms
+ *   of NAPI/rusqlite/OS-page-cache init plus the cost of walking through
+ *   fixture files added by new language extractors. Local v3.9.6 vs HEAD
+ *   on the same corpus measured 78.8ms vs 67.5ms single-shot (HEAD faster),
+ *   while the warmed `queries.fnDepsMs` in the same benchmark showed 4.0ms
+ *   vs 2.8ms — confirming no underlying regression. Methodology fixed in
+ *   #1113: queryTimeMs now uses 3 warmup runs + median of 5 with
+ *   `noTests: true`, matching query-benchmark.ts hygiene. Exemption kept
+ *   in place until 3.11.0+ data captures the new steady-state under the
+ *   updated methodology (expected ~36ms native on this corpus); remove
+ *   the entry then.
  *
  * - 3.10.0:fnDeps depth 5 — same cause as Query time above. Merging main
  *   into #1102 added the Erlang extractor (#1103) on top of the existing