diff --git a/.changeset/wise-jays-romp.md b/.changeset/wise-jays-romp.md
new file mode 100644
index 000000000..dddaff2ad
--- /dev/null
+++ b/.changeset/wise-jays-romp.md
@@ -0,0 +1,5 @@
+---
+type: Fixed
+pr: 3098
+---
+**`phase_id_convention` set in `.planning/config.json` is no longer silently dropped** — the config loader's resolved-config constructor omitted the key despite it being in the valid-keys manifest, so the milestone-prefix validation check could only be activated via the ROADMAP frontmatter fallback. The key now survives resolution. (#2997)
diff --git a/src/config-loader.cts b/src/config-loader.cts
index 6159709a6..cf0a95594 100644
--- a/src/config-loader.cts
+++ b/src/config-loader.cts
@@ -812,6 +812,7 @@ function loadConfigResolved(cwd: string, options: Record<string, unknown> = {}):
       response_language: get('response_language') || null,
       claude_md_path: get('claude_md_path') || null,
       claude_md_assembly: (parsed['claude_md_assembly']) || null,
+      phase_id_convention: get('phase_id_convention') ?? null,
     };
 
     // ADR-857 phase 3b: federated config overlay
diff --git a/tests/config-loader.test.cjs b/tests/config-loader.test.cjs
index e0a545528..f10c57e8a 100644
--- a/tests/config-loader.test.cjs
+++ b/tests/config-loader.test.cjs
@@ -1255,3 +1255,44 @@ describe("loadConfigResolved — corrupt config is distinguishable from absent",
     assert.equal(res.degraded, false, "an empty file is not corruption");
   });
 });
+
+// ─── #2997: phase_id_convention survives config resolution ─────────────────
+
+describe('#2997: phase_id_convention is not silently dropped on a clean read', () => {
+  const { createTempDir } = require('./helpers.cjs');
+  const cfgPath = (dir) => path.join(dir, '.planning', 'config.json');
+
+  test('setting phase_id_convention in config.json survives into the resolved config', () => {
+    const tmpDir = createTempDir('gsd-2997-');
+    try {
+      fs.mkdirSync(path.join(tmpDir, '.planning'), { recursive: true });
+      fs.writeFileSync(cfgPath(tmpDir), JSON.stringify({ phase_id_convention: 'milestone-prefixed' }), 'utf-8');
+      const res = loadConfigResolved(tmpDir);
+      assert.equal(res.degraded, false, 'read must report as non-degraded');
+      assert.equal(res.config.phase_id_convention, 'milestone-prefixed',
+        `phase_id_convention must survive resolution; got: ${JSON.stringify(res.config.phase_id_convention)}`);
+    } finally { cleanup(tmpDir); }
+  });
+
+  test('phase_id_convention set to null round-trips correctly', () => {
+    const tmpDir = createTempDir('gsd-2997-null-');
+    try {
+      fs.mkdirSync(path.join(tmpDir, '.planning'), { recursive: true });
+      fs.writeFileSync(cfgPath(tmpDir), JSON.stringify({ phase_id_convention: null }), 'utf-8');
+      const res = loadConfigResolved(tmpDir);
+      assert.equal(res.config.phase_id_convention, null,
+        'null phase_id_convention must round-trip as null');
+    } finally { cleanup(tmpDir); }
+  });
+
+  test('phase_id_convention absent → null in resolved config (no false default)', () => {
+    const tmpDir = createTempDir('gsd-2997-absent-');
+    try {
+      fs.mkdirSync(path.join(tmpDir, '.planning'), { recursive: true });
+      fs.writeFileSync(cfgPath(tmpDir), JSON.stringify({ commit_docs: true }), 'utf-8');
+      const res = loadConfigResolved(tmpDir);
+      assert.equal(res.config.phase_id_convention, null,
+        'absent phase_id_convention must resolve to null, not undefined');
+    } finally { cleanup(tmpDir); }
+  });
+});