diff --git a/src/config/config.legacy-config-detection.rejects-routing-allowfrom.test.ts b/src/config/config.legacy-config-detection.rejects-routing-allowfrom.test.ts
index c41f2f6495..1ef9bfb68f 100644
--- a/src/config/config.legacy-config-detection.rejects-routing-allowfrom.test.ts
+++ b/src/config/config.legacy-config-detection.rejects-routing-allowfrom.test.ts
@@ -210,7 +210,7 @@ describe("legacy config detection", () => {
       },
     });
     expect(res.changes).toContain(
-      "Merged memorySearch → agents.defaults.memorySearch (preserved explicit agents.defaults overrides).",
+      "Merged memorySearch → agents.defaults.memorySearch (filled missing fields from legacy; kept explicit agents.defaults values).",
     );
     expect(res.config?.agents?.defaults?.memorySearch).toMatchObject({
       provider: "openai",
@@ -219,6 +219,37 @@ describe("legacy config detection", () => {
       query: { maxResults: 7 },
     });
   });
+  it("keeps nested agents.defaults.memorySearch values when merging legacy defaults", async () => {
+    vi.resetModules();
+    const { migrateLegacyConfig } = await import("./config.js");
+    const res = migrateLegacyConfig({
+      memorySearch: {
+        query: {
+          maxResults: 7,
+          minScore: 0.25,
+          hybrid: { enabled: true, textWeight: 0.8, vectorWeight: 0.2 },
+        },
+      },
+      agents: {
+        defaults: {
+          memorySearch: {
+            query: {
+              maxResults: 3,
+              hybrid: { enabled: false },
+            },
+          },
+        },
+      },
+    });
+
+    expect(res.config?.agents?.defaults?.memorySearch).toMatchObject({
+      query: {
+        maxResults: 3,
+        minScore: 0.25,
+        hybrid: { enabled: false, textWeight: 0.8, vectorWeight: 0.2 },
+      },
+    });
+  });
   it("migrates tools.bash to tools.exec", async () => {
     vi.resetModules();
     const { migrateLegacyConfig } = await import("./config.js");
diff --git a/src/config/legacy.migrations.part-3.ts b/src/config/legacy.migrations.part-3.ts
index a762f74141..18db0da19c 100644
--- a/src/config/legacy.migrations.part-3.ts
+++ b/src/config/legacy.migrations.part-3.ts
@@ -30,10 +30,12 @@ export const LEGACY_CONFIG_MIGRATIONS_PART_3: LegacyConfigMigration[] = [
         defaults.memorySearch = legacyMemorySearch;
         changes.push("Moved memorySearch → agents.defaults.memorySearch.");
       } else {
-        mergeMissing(existing, legacyMemorySearch);
-        defaults.memorySearch = existing;
+        // agents.defaults stays authoritative; legacy top-level config only fills gaps.
+        const merged = structuredClone(existing);
+        mergeMissing(merged, legacyMemorySearch);
+        defaults.memorySearch = merged;
         changes.push(
-          "Merged memorySearch → agents.defaults.memorySearch (preserved explicit agents.defaults overrides).",
+          "Merged memorySearch → agents.defaults.memorySearch (filled missing fields from legacy; kept explicit agents.defaults values).",
         );
       }