diff --git a/bin/mcp-server.mjs b/bin/mcp-server.mjs
index 2a79f151d6..39590d379c 100644
--- a/bin/mcp-server.mjs
+++ b/bin/mcp-server.mjs
@@ -3,7 +3,7 @@
 import { spawn } from "node:child_process";
 import { existsSync } from "node:fs";
 import { dirname, join } from "node:path";
-import { fileURLToPath } from "node:url";
+import { fileURLToPath, pathToFileURL } from "node:url";
 
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = dirname(__filename);
@@ -43,7 +43,15 @@ export async function startMcpCli(rootDir = ROOT) {
   }
 
   // `tsx` loader is only required for local `.ts` fallback; JS entry works without it.
-  const loaderArgs = mcpEntry.endsWith(".ts") ? ["--import", "tsx"] : [];
+  const tsxLoaderArgs = mcpEntry.endsWith(".ts") ? ["--import", "tsx"] : [];
+  // Preload the stdout/stderr console guard before mcpEntry's own module graph evaluates —
+  // DB init (a side effect of createMcpServer()'s tool registration) logs via plain
+  // console.log, and by the time any code inside mcpEntry itself could redirect it, that
+  // module's own (hoisted) imports have already run. Loading the guard first, in a separate
+  // module, is the only point early enough to guarantee it never leaks into the JSON-RPC
+  // stream on stdout.
+  const consoleGuard = pathToFileURL(join(__dirname, "mcpStdioConsoleGuard.mjs")).href;
+  const loaderArgs = ["--import", consoleGuard, ...tsxLoaderArgs];
 
   await new Promise((resolve, reject) => {
     const child = spawn(process.execPath, [...loaderArgs, mcpEntry], {
diff --git a/bin/mcpStdioConsoleGuard.mjs b/bin/mcpStdioConsoleGuard.mjs
new file mode 100644
index 0000000000..074dd1e416
--- /dev/null
+++ b/bin/mcpStdioConsoleGuard.mjs
@@ -0,0 +1,16 @@
+// Preloaded (via `node --import`) before open-sse/mcp-server/server.ts and its entire
+// import graph evaluate. The stdio MCP transport uses stdout exclusively for JSON-RPC
+// messages, but DB init (getDbInstance(), triggered as a side effect of evaluating the
+// server's module graph — e.g. tool registration reading compression settings) logs via
+// plain console.log. A redirect placed *inside* server.ts (even at the top of its first
+// executed function) is too late: static imports are hoisted and fully evaluated before
+// any of that function's own code runs, so earlier console.log calls during import-time
+// side effects already escaped to the real stdout by then. Redirecting here, in a module
+// that loads before server.ts is even requested, is the only point early enough to
+// guarantee no startup output leaks into the JSON-RPC stream and corrupts it client-side
+// (e.g. Claude Desktop: "Unexpected token 'D', \"[DB] Changi\"... is not valid JSON").
+import { Console } from "node:console";
+
+const stderrConsole = new Console({ stdout: process.stderr, stderr: process.stderr });
+console.log = stderrConsole.log.bind(stderrConsole);
+console.warn = stderrConsole.warn.bind(stderrConsole);
diff --git a/bin/omniroute.mjs b/bin/omniroute.mjs
index fa216bb3ff..c5b280ba64 100755
--- a/bin/omniroute.mjs
+++ b/bin/omniroute.mjs
@@ -43,6 +43,19 @@ if (isVersionFastPath(process.argv)) {
   process.exit(0);
 }
 
+// MCP stdio transport uses stdout exclusively for JSON-RPC messages. Redirect
+// console.log/warn to stderr before anything else runs — including the tsx/esm and
+// polyfill imports below, since those (and their transitive module graphs, e.g. DB
+// init) can themselves log during evaluation. Redirecting after those imports let
+// early output leak straight into the JSON-RPC stream and corrupt it client-side
+// (e.g. Claude Desktop: "Unexpected token 'D', \"[DB] Changi\"... is not valid JSON").
+if (process.argv.includes("--mcp")) {
+  const { Console } = await import("node:console");
+  const stderrConsole = new Console({ stdout: process.stderr, stderr: process.stderr });
+  console.log = stderrConsole.log.bind(stderrConsole);
+  console.warn = stderrConsole.warn.bind(stderrConsole);
+}
+
 // Register tsx so dynamic imports of .ts source files (referenced as .js per
 // TypeScript conventions) resolve correctly. The build never emits .js for
 // src/lib/cli-helper/, so tsx handles the .ts → .js resolution at runtime.
@@ -58,16 +71,6 @@ await import("../open-sse/utils/setupPolyfill.ts");
 const { registerAliasResolver } = await import("./aliasResolver.mjs");
 await registerAliasResolver(ROOT);
 
-// MCP stdio transport uses stdout exclusively for JSON-RPC messages.
-// Redirect console.log/warn to stderr early (before loadEnvFile and DB init)
-// so no startup output corrupts the protocol.
-if (process.argv.includes("--mcp")) {
-  const { Console } = await import("node:console");
-  const stderrConsole = new Console({ stdout: process.stderr, stderr: process.stderr });
-  console.log = stderrConsole.log.bind(stderrConsole);
-  console.warn = stderrConsole.warn.bind(stderrConsole);
-}
-
 // Electron persists secrets (JWT_SECRET, API_KEY_SECRET, STORAGE_ENCRYPTION_KEY) to
 // `<DATA_DIR>/server.env` (electron/main.js), never `.env`. Migrating an existing
 // install (storage.sqlite + server.env) to the CLI left those secrets undiscoverable —
diff --git a/open-sse/mcp-server/server.ts b/open-sse/mcp-server/server.ts
index d37a157f71..d61b654f3c 100644
--- a/open-sse/mcp-server/server.ts
+++ b/open-sse/mcp-server/server.ts
@@ -1403,6 +1403,10 @@ export function createMcpServer(): McpServer {
  * Called when `omniroute --mcp` is used.
  */
 export async function startMcpStdio(): Promise<void> {
+  // Stdout is reserved for JSON-RPC — bin/mcpStdioConsoleGuard.mjs is preloaded via
+  // `node --import` (see bin/mcp-server.mjs) so console.log/warn already redirect to
+  // stderr before this module's own imports evaluate (DB init happens as a side effect of
+  // createMcpServer()'s tool registration, earlier than any code placed here could catch).
   const server = createMcpServer();
   const transport = new StdioServerTransport();
   const version = process.env.npm_package_version || "1.8.1";
diff --git a/tests/unit/mcp-stdio-json-purity.test.ts b/tests/unit/mcp-stdio-json-purity.test.ts
new file mode 100644
index 0000000000..e91cad7316
--- /dev/null
+++ b/tests/unit/mcp-stdio-json-purity.test.ts
@@ -0,0 +1,76 @@
+import { describe, it } from "node:test";
+import assert from "node:assert/strict";
+import { spawn } from "node:child_process";
+import { join } from "node:path";
+
+const ROOT = new URL("../..", import.meta.url).pathname.replace(/^\/([A-Za-z]:)/, "$1");
+
+/**
+ * Regression coverage: `omniroute --mcp` (the stdio transport Claude Desktop and other MCP
+ * clients spawn) must write nothing but JSON-RPC to stdout. DB init — a side effect of
+ * `createMcpServer()`'s tool registration reading compression settings — used to log via
+ * plain `console.log` before any redirect was in place (ES module static imports are hoisted
+ * and evaluate before any code inside the importing module's own functions runs, so a
+ * redirect placed inside server.ts itself was too late). That leaked lines like
+ * "[DB] Changing cache_size from 65536KB to 16384KB" straight onto stdout, corrupting the
+ * JSON-RPC stream client-side (e.g. Claude Desktop: `Unexpected token 'D', "[DB] Changi"...
+ * is not valid JSON`). Fixed by preloading bin/mcpStdioConsoleGuard.mjs via `node --import`
+ * (bin/mcp-server.mjs) — the only point early enough to run before the MCP entry's module
+ * graph evaluates at all.
+ */
+describe("omniroute --mcp stdio transport", () => {
+  it("writes only valid JSON-RPC to stdout — no DB init or other startup logging leaks through", async () => {
+    const child = spawn(
+      process.execPath,
+      [join(ROOT, "bin", "omniroute.mjs"), "--mcp"],
+      { cwd: ROOT, env: process.env }
+    );
+
+    let stdout = "";
+    let stderr = "";
+    child.stdout.on("data", (chunk) => {
+      stdout += chunk.toString();
+    });
+    child.stderr.on("data", (chunk) => {
+      stderr += chunk.toString();
+    });
+
+    child.stdin.write(
+      `${JSON.stringify({
+        jsonrpc: "2.0",
+        id: 1,
+        method: "initialize",
+        params: {
+          protocolVersion: "2025-03-26",
+          capabilities: {},
+          clientInfo: { name: "regression-test", version: "0" },
+        },
+      })}\n`
+    );
+
+    await new Promise((resolve) => setTimeout(resolve, 4000));
+    child.kill();
+
+    const stdoutLines = stdout.split("\n").filter((line) => line.trim().length > 0);
+    assert.ok(stdoutLines.length > 0, "expected at least one line on stdout (the initialize response)");
+
+    for (const line of stdoutLines) {
+      assert.doesNotThrow(
+        () => JSON.parse(line),
+        `stdout line is not valid JSON (startup logging leaked onto stdout): ${line.slice(0, 120)}`
+      );
+    }
+
+    const initResponse = stdoutLines
+      .map((line) => JSON.parse(line))
+      .find((msg) => msg.id === 1);
+    assert.ok(initResponse, "expected an initialize response with id 1 on stdout");
+    assert.equal(initResponse.jsonrpc, "2.0");
+
+    // The DB init logging must still happen — just on stderr, not stdout.
+    assert.ok(
+      stderr.includes("[DB]"),
+      "expected DB init logging on stderr (proves it was redirected, not silently dropped)"
+    );
+  });
+});