diff --git a/src/plugins/manifest-registry.test.ts b/src/plugins/manifest-registry.test.ts
index 9212c6fcf05..7779870c00d 100644
--- a/src/plugins/manifest-registry.test.ts
+++ b/src/plugins/manifest-registry.test.ts
@@ -150,7 +150,65 @@ describe("loadPluginManifestRegistry", () => {
       }),
     ];
 
-    expect(countDuplicateWarnings(loadRegistry(candidates))).toBe(1);
+    const registry = loadRegistry(candidates);
+    expect(countDuplicateWarnings(registry)).toBe(1);
+    // Only one record should be kept to prevent Gateway instability
+    expect(registry.plugins.filter((p) => p.id === "test-plugin")).toHaveLength(1);
+  });
+
+  it("keeps higher-precedence origin when genuine duplicate is detected from different paths", () => {
+    const bundledDir = makeTempDir();
+    const globalDir = makeTempDir();
+    const manifest = { id: "feishu-dup", configSchema: { type: "object" } };
+    writeManifest(bundledDir, manifest);
+    writeManifest(globalDir, manifest);
+
+    // Bundled discovered first, then global (npm-installed copy)
+    const candidates: PluginCandidate[] = [
+      createPluginCandidate({
+        idHint: "feishu-dup",
+        rootDir: bundledDir,
+        origin: "bundled",
+      }),
+      createPluginCandidate({
+        idHint: "feishu-dup",
+        rootDir: globalDir,
+        origin: "global",
+      }),
+    ];
+
+    const registry = loadRegistry(candidates);
+    expect(countDuplicateWarnings(registry)).toBe(1);
+    expect(registry.plugins.filter((p) => p.id === "feishu-dup")).toHaveLength(1);
+    // Global has higher precedence than bundled (config > workspace > global > bundled)
+    expect(registry.plugins[0]?.origin).toBe("global");
+  });
+
+  it("keeps existing record when genuine duplicate has lower precedence", () => {
+    const configDir = makeTempDir();
+    const globalDir = makeTempDir();
+    const manifest = { id: "lower-prec", configSchema: { type: "object" } };
+    writeManifest(configDir, manifest);
+    writeManifest(globalDir, manifest);
+
+    const candidates: PluginCandidate[] = [
+      createPluginCandidate({
+        idHint: "lower-prec",
+        rootDir: configDir,
+        origin: "config",
+      }),
+      createPluginCandidate({
+        idHint: "lower-prec",
+        rootDir: globalDir,
+        origin: "global",
+      }),
+    ];
+
+    const registry = loadRegistry(candidates);
+    expect(countDuplicateWarnings(registry)).toBe(1);
+    expect(registry.plugins.filter((p) => p.id === "lower-prec")).toHaveLength(1);
+    // Config has higher precedence, should be kept
+    expect(registry.plugins[0]?.origin).toBe("config");
   });
 
   it("suppresses duplicate warning when candidates share the same physical directory via symlink", () => {
diff --git a/src/plugins/manifest-registry.ts b/src/plugins/manifest-registry.ts
index d392144f925..db91697c23a 100644
--- a/src/plugins/manifest-registry.ts
+++ b/src/plugins/manifest-registry.ts
@@ -233,8 +233,22 @@ export function loadPluginManifestRegistry(params: {
         level: "warn",
         pluginId: manifest.id,
         source: candidate.source,
-        message: `duplicate plugin id detected; later plugin may be overridden (${candidate.source})`,
+        message: `duplicate plugin id detected; skipping duplicate from ${candidate.source}`,
       });
+      // Genuine duplicate from a different physical path: apply the same
+      // precedence logic as same-path duplicates to avoid registering two
+      // records with the same plugin id (which causes Gateway instability).
+      if (PLUGIN_ORIGIN_RANK[candidate.origin] < PLUGIN_ORIGIN_RANK[existing.candidate.origin]) {
+        records[existing.recordIndex] = buildRecord({
+          manifest,
+          candidate,
+          manifestPath: manifestRes.manifestPath,
+          schemaCacheKey,
+          configSchema,
+        });
+        seenIds.set(manifest.id, { candidate, recordIndex: existing.recordIndex });
+      }
+      continue;
     } else {
       seenIds.set(manifest.id, { candidate, recordIndex: records.length });
     }