diff --git a/gitnexus/src/cli/mcp.ts b/gitnexus/src/cli/mcp.ts
index 3bc708087..eccbb4318 100644
--- a/gitnexus/src/cli/mcp.ts
+++ b/gitnexus/src/cli/mcp.ts
@@ -31,12 +31,15 @@ export const mcpCommand = async () => {
 
   const repos = await backend.listRepos();
   if (repos.length === 0) {
-    logger.error(
+    // Operator-actionable but the server still starts and serves; warn-level,
+    // not error. Tools will discover newly-analyzed repos via lazy refresh.
+    logger.warn(
       'GitNexus: No indexed repos yet. Run `gitnexus analyze` in a git repo — the server will pick it up automatically.',
     );
   } else {
-    logger.error(
-      `GitNexus: MCP server starting with ${repos.length} repo(s): ${repos.map((r) => r.name).join(', ')}`,
+    logger.info(
+      { repoCount: repos.length, repos: repos.map((r) => r.name) },
+      'GitNexus: MCP server starting',
     );
   }
 
diff --git a/gitnexus/src/core/ingestion/workers/worker-pool.ts b/gitnexus/src/core/ingestion/workers/worker-pool.ts
index bcc9aa544..b6f16de66 100644
--- a/gitnexus/src/core/ingestion/workers/worker-pool.ts
+++ b/gitnexus/src/core/ingestion/workers/worker-pool.ts
@@ -260,10 +260,17 @@ export const createWorkerPool = (
             timeoutMs: nextTimeout,
           };
           logger.warn(
-            `Worker ${workerIndex} parse job idle timeout after ${job.timeoutMs / 1000}s ` +
-              `(${job.items.length} items, ${job.estimatedBytes} bytes, last progress: ${lastProgress}). ` +
-              `Splitting into ${first.items.length}/${second.items.length} item jobs with ` +
-              `${nextTimeout / 1000}s timeout.`,
+            {
+              workerIndex,
+              timeoutSec: job.timeoutMs / 1000,
+              items: job.items.length,
+              estimatedBytes: job.estimatedBytes,
+              lastProgress,
+              firstSplitItems: first.items.length,
+              secondSplitItems: second.items.length,
+              nextTimeoutSec: nextTimeout / 1000,
+            },
+            `Worker ${workerIndex} parse job idle timeout. Splitting into ${first.items.length}/${second.items.length} item jobs.`,
           );
           // Preserve intuitive retry order; final result order is still enforced by startIndex sort.
           jobs.unshift(first, second);
@@ -273,9 +280,14 @@ export const createWorkerPool = (
         const nextAttempt = job.attempt + 1;
         if (nextAttempt <= poolOptions.maxTimeoutRetries) {
           logger.warn(
-            `Worker ${workerIndex} parse job idle timeout after ${job.timeoutMs / 1000}s ` +
-              `(single item, attempt ${nextAttempt}/${poolOptions.maxTimeoutRetries + 1}). ` +
-              `Retrying with ${nextTimeout / 1000}s timeout.`,
+            {
+              workerIndex,
+              timeoutSec: job.timeoutMs / 1000,
+              attempt: nextAttempt,
+              maxAttempts: poolOptions.maxTimeoutRetries + 1,
+              nextTimeoutSec: nextTimeout / 1000,
+            },
+            `Worker ${workerIndex} parse job idle timeout (single item). Retrying with ${nextTimeout / 1000}s timeout.`,
           );
           jobs.unshift({
             ...job,
diff --git a/gitnexus/src/core/logger.ts b/gitnexus/src/core/logger.ts
index d97146a61..3230b91a5 100644
--- a/gitnexus/src/core/logger.ts
+++ b/gitnexus/src/core/logger.ts
@@ -69,6 +69,10 @@ function tryBuildPrettyTransport(): LoggerOptions['transport'] | undefined {
     return {
       target: 'pino-pretty',
       options: {
+        // Route to stderr (fd 2) so pretty output doesn't contaminate
+        // CLI tool data on stdout (fd 1). pino-pretty's default is fd 1,
+        // which would interleave with `gitnexus query | jq` output.
+        destination: 2,
         colorize: true,
         translateTime: 'SYS:HH:MM:ss.l',
         ignore: 'pid,hostname',
diff --git a/gitnexus/src/mcp/local/local-backend.ts b/gitnexus/src/mcp/local/local-backend.ts
index fade093ea..47dbf31dd 100644
--- a/gitnexus/src/mcp/local/local-backend.ts
+++ b/gitnexus/src/mcp/local/local-backend.ts
@@ -165,29 +165,27 @@ const confidenceForRelType = (relType: string | undefined): number =>
 /** Structured error logging for query failures — replaces empty catch blocks */
 function logQueryError(context: string, err: unknown): void {
   const msg = err instanceof Error ? err.message : String(err);
-  logger.error(`GitNexus [${context}]: ${msg}`);
+  logger.error({ context, err: msg }, 'GitNexus query failed');
 }
 
 /**
- * Structured per-query latency log for production aggregation (#553).
+ * Per-query latency telemetry for production aggregation (#553).
  *
- * Emitted on stderr — NOT stdout — because the MCP stdio transport uses
- * stdout exclusively for JSON-RPC responses (#324), and the CLI e2e test
- * `tool output goes to stdout via fd 1` asserts that stdout parses cleanly
- * as JSON. Any `console.log` from inside a tool handler would corrupt the
- * protocol. Matches the existing `logQueryError` convention above, which
- * uses stderr for the same reason.
+ * Logged at `debug` level — timing is observability/telemetry, not an
+ * error. Operators wanting per-query timing set `GITNEXUS_LOG_LEVEL=debug`
+ * (or equivalent). Emitting at `error` level (the original migration
+ * artifact) caused alerting rules to fire on every successful query and
+ * inflated stderr noise for every MCP/CLI invocation.
  *
- * The `GitNexus [query:timing] …` prefix keeps lines greppable; the
- * `phases` payload is JSON so log-scraping pipelines can parse it
- * without custom format knowledge.
+ * Emitted via the project logger which routes to stderr — never stdout —
+ * because the MCP stdio transport uses stdout exclusively for JSON-RPC
+ * responses (#324) and the CLI e2e test `tool output goes to stdout via
+ * fd 1` asserts stdout parses cleanly as JSON.
  */
 function logQueryTiming(query: string, phases: Record<string, number>): void {
   const totalMs = phases.wall ?? Object.values(phases).reduce((a, b) => a + b, 0);
   const truncated = query.length > 80 ? `${query.slice(0, 80)}…` : query;
-  logger.error(
-    `GitNexus [query:timing] query=${JSON.stringify(truncated)} totalMs=${totalMs} phases=${JSON.stringify(phases)}`,
-  );
+  logger.debug({ query: truncated, totalMs, phases }, 'GitNexus query timing');
 }
 
 export interface CodebaseContext {