diff --git a/.changeset/3600-milestone-phase-filter-project-code.md b/.changeset/3600-milestone-phase-filter-project-code.md
new file mode 100644
index 000000000..17fdb6609
--- /dev/null
+++ b/.changeset/3600-milestone-phase-filter-project-code.md
@@ -0,0 +1,5 @@
+---
+type: Fixed
+issue: 3600
+---
+**`init.new-milestone` now counts project-code-prefixed phase directories** — `getMilestonePhaseFilter` previously skipped `.planning/phases/CK-01-name` against a numeric ROADMAP heading like `### Phase 1:`: the numeric matcher required the directory name to start with a digit and the custom-ID matcher compared the full prefixed name against the bare milestone token. Added a strip-and-retry path that strips the same `^[A-Z]{1,6}-(?=\d)` prefix `normalizePhaseName` already recognises and retries the numeric match. The fix lands in both the CJS runtime (`get-shit-done/bin/lib/core.cjs:isDirInMilestone`) and the SDK twin (`sdk/src/query/state.ts:isDirInMilestone`), and is shared by every caller of `getMilestonePhaseFilter` — including `init.new-milestone`, `phase complete`, `verify-work`, and `validate-health`.
diff --git a/get-shit-done/bin/lib/core.cjs b/get-shit-done/bin/lib/core.cjs
index f3809e9d4..71adb0ac0 100644
--- a/get-shit-done/bin/lib/core.cjs
+++ b/get-shit-done/bin/lib/core.cjs
@@ -1748,6 +1748,18 @@ function getMilestonePhaseFilter(cwd, versionOverride) {
     // Try custom ID match (e.g. PROJ-42-description → PROJ-42)
     const customMatch = dirName.match(/^([A-Za-z][A-Za-z0-9]*(?:-[A-Za-z0-9]+)*)/);
     if (customMatch && normalized.has(customMatch[1].toLowerCase())) return true;
+    // #3600: project-code-prefixed directory (`CK-01-name`) against a
+    // numeric ROADMAP heading (`### Phase 1:`). Strip the same prefix
+    // shape `normalizePhaseName` recognises (`^[A-Z]{1,6}-(?=\d)`) and
+    // retry the numeric match. This runs AFTER the custom-ID match so
+    // a roadmap that uses `Phase PROJ-42:` continues to win via the
+    // existing custom-ID path; the strip-and-retry only fires when the
+    // milestone is keyed on the bare numeric form.
+    const stripped = dirName.replace(/^[A-Z]{1,6}-(?=\d)/i, '');
+    if (stripped !== dirName) {
+      const sm = stripped.match(/^0*(\d+[A-Za-z]?(?:\.\d+)*)/);
+      if (sm && normalized.has(sm[1].toLowerCase())) return true;
+    }
     return false;
   }
   isDirInMilestone.phaseCount = milestonePhaseNums.size;
diff --git a/sdk/src/query/state.ts b/sdk/src/query/state.ts
index 3c855e1f9..1c97659a7 100644
--- a/sdk/src/query/state.ts
+++ b/sdk/src/query/state.ts
@@ -71,6 +71,18 @@ export async function getMilestonePhaseFilter(projectDir: string, workstream?: s
     // Try custom ID match
     const customMatch = dirName.match(/^([A-Za-z][A-Za-z0-9]*(?:-[A-Za-z0-9]+)*)/);
     if (customMatch && normalized.has(customMatch[1].toLowerCase())) return true;
+    // #3600: project-code-prefixed directory (`CK-01-name`) against a
+    // numeric ROADMAP heading (`### Phase 1:`). Strip the same prefix
+    // shape `normalizePhaseName` recognises (`^[A-Z]{1,6}-(?=\d)`) and
+    // retry the numeric match. This runs AFTER the custom-ID match so
+    // a roadmap that uses `Phase PROJ-42:` continues to win via the
+    // existing custom-ID path; the strip-and-retry only fires when the
+    // milestone is keyed on the bare numeric form.
+    const stripped = dirName.replace(/^[A-Z]{1,6}-(?=\d)/i, '');
+    if (stripped !== dirName) {
+      const sm = stripped.match(/^0*(\d+[A-Za-z]?(?:\.\d+)*)/);
+      if (sm && normalized.has(sm[1].toLowerCase())) return true;
+    }
     return false;
   }) as ((dirName: string) => boolean) & { phaseCount: number };
 
diff --git a/tests/bug-3600-milestone-phase-filter-project-code-prefix.test.cjs b/tests/bug-3600-milestone-phase-filter-project-code-prefix.test.cjs
new file mode 100644
index 000000000..3b0aabc83
--- /dev/null
+++ b/tests/bug-3600-milestone-phase-filter-project-code-prefix.test.cjs
@@ -0,0 +1,177 @@
+/**
+ * Bug #3600: `init.new-milestone` reports `phase_dir_count: 0` for
+ * project-code-prefixed phase directories (e.g. `.planning/phases/CK-01-name`)
+ * against a ROADMAP that uses numeric `Phase 1:` headings.
+ *
+ * Root cause: `getMilestonePhaseFilter` builds an `isDirInMilestone(dirName)`
+ * predicate that tries two paths:
+ *   1) Numeric match — requires the directory name to START with a digit;
+ *      `CK-01-name` starts with `C`, so this path skips.
+ *   2) Custom-ID match — captures the leading token (`CK-01-name` as a
+ *      whole) and compares it to the normalised milestone phase IDs
+ *      (`1`). No match.
+ *
+ * The predicate has no path that strips a project-code prefix before the
+ * numeric match. This fix adds that third path: when both existing
+ * matches fail, strip an optional `^[A-Z]{1,6}-(?=\d)` prefix (the same
+ * shape `normalizePhaseName` already strips) and retry the numeric match.
+ *
+ * The fix is shared between the CJS impl in `core.cjs` and the SDK twin
+ * in `sdk/src/query/state.ts`. The behavioural test exercises the CJS
+ * surface (the active runtime).
+ */
+
+'use strict';
+
+process.env.GSD_TEST_MODE = '1';
+
+const { describe, test, beforeEach, afterEach } = require('node:test');
+const assert = require('node:assert/strict');
+const fs = require('node:fs');
+const path = require('node:path');
+const { runGsdTools, createTempProject, cleanup } = require('./helpers.cjs');
+
+function writeRoadmap(tmpDir, body) {
+  fs.writeFileSync(path.join(tmpDir, '.planning', 'ROADMAP.md'), body);
+}
+function writeState(tmpDir, version) {
+  fs.writeFileSync(
+    path.join(tmpDir, '.planning', 'STATE.md'),
+    `---\nmilestone: ${version}\n---\n`,
+  );
+}
+function writeConfig(tmpDir, configObj) {
+  fs.writeFileSync(
+    path.join(tmpDir, '.planning', 'config.json'),
+    JSON.stringify(configObj, null, 2),
+  );
+}
+function ensurePhaseDir(tmpDir, name) {
+  fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', name), { recursive: true });
+}
+
+describe('bug #3600: milestone phase filter understands project-code-prefixed directories', () => {
+  let tmpDir;
+  beforeEach(() => {
+    tmpDir = createTempProject('bug-3600-');
+  });
+  afterEach(() => {
+    cleanup(tmpDir);
+  });
+
+  test('init.new-milestone counts CK-NN-name dirs against numeric `Phase N:` headings', () => {
+    writeConfig(tmpDir, { project_code: 'CK' });
+    writeState(tmpDir, 'v1.0.0');
+    writeRoadmap(
+      tmpDir,
+      [
+        '# Roadmap',
+        '',
+        '## Current Milestone: v1.0.0 - Test',
+        '',
+        '### Phase 1: Discovery',
+        '**Goal:** GoalOne',
+        '',
+        '### Phase 2: Build',
+        '**Goal:** GoalTwo',
+        '',
+      ].join('\n'),
+    );
+    ensurePhaseDir(tmpDir, 'CK-01-discovery');
+    ensurePhaseDir(tmpDir, 'CK-02-build');
+
+    const r = runGsdTools(['init', 'new-milestone', '--json'], tmpDir);
+    assert.ok(r.success, `init new-milestone failed: ${r.error || r.output}`);
+    const payload = JSON.parse(r.output);
+    assert.strictEqual(
+      payload.phase_dir_count,
+      2,
+      `expected phase_dir_count=2 for two CK-NN-name dirs against Phase 1/Phase 2 headings, got ${payload.phase_dir_count}`,
+    );
+  });
+
+  test('unprefixed directories continue to count (#3537 / existing contract)', () => {
+    writeState(tmpDir, 'v1.0.0');
+    writeRoadmap(
+      tmpDir,
+      [
+        '# Roadmap',
+        '',
+        '## Current Milestone: v1.0.0 - Test',
+        '',
+        '### Phase 1: First',
+        '**Goal:** g',
+        '',
+      ].join('\n'),
+    );
+    ensurePhaseDir(tmpDir, '01-first');
+
+    const r = runGsdTools(['init', 'new-milestone', '--json'], tmpDir);
+    assert.ok(r.success);
+    const payload = JSON.parse(r.output);
+    assert.strictEqual(payload.phase_dir_count, 1);
+  });
+
+  test('custom-ID match for PROJ-42 directory + Phase PROJ-42: heading still works', () => {
+    // Existing custom-ID path: directory name exactly equals the custom
+    // phase ID (no slug suffix). The PROJ-42 → Phase PROJ-42: match must
+    // continue to fire via the second branch of `isDirInMilestone`, not
+    // get pre-empted by the new strip-and-retry branch.
+    writeConfig(tmpDir, { project_code: 'PROJ' });
+    writeState(tmpDir, 'v1.0.0');
+    writeRoadmap(
+      tmpDir,
+      [
+        '# Roadmap',
+        '',
+        '## Current Milestone: v1.0.0 - Test',
+        '',
+        '### Phase PROJ-42: Custom',
+        '**Goal:** g',
+        '',
+      ].join('\n'),
+    );
+    ensurePhaseDir(tmpDir, 'PROJ-42');
+
+    const r = runGsdTools(['init', 'new-milestone', '--json'], tmpDir);
+    assert.ok(r.success);
+    const payload = JSON.parse(r.output);
+    assert.strictEqual(
+      payload.phase_dir_count,
+      1,
+      'PROJ-42 directory must still match Phase PROJ-42: via the custom-ID path',
+    );
+  });
+
+  test('directories that do not match the milestone do NOT count', () => {
+    // Counter-test: a 999-backlog directory or a totally-unrelated phase
+    // must NOT be counted in the milestone tally.
+    writeConfig(tmpDir, { project_code: 'CK' });
+    writeState(tmpDir, 'v1.0.0');
+    writeRoadmap(
+      tmpDir,
+      [
+        '# Roadmap',
+        '',
+        '## Current Milestone: v1.0.0 - Test',
+        '',
+        '### Phase 1: First',
+        '**Goal:** g',
+        '',
+      ].join('\n'),
+    );
+    ensurePhaseDir(tmpDir, 'CK-01-first');
+    // Future / backlog phases that should not be counted in this milestone.
+    ensurePhaseDir(tmpDir, 'CK-99-backlog');
+    ensurePhaseDir(tmpDir, 'CK-100-future');
+
+    const r = runGsdTools(['init', 'new-milestone', '--json'], tmpDir);
+    assert.ok(r.success);
+    const payload = JSON.parse(r.output);
+    assert.strictEqual(
+      payload.phase_dir_count,
+      1,
+      'only CK-01-first should match Phase 1; CK-99 and CK-100 must be excluded',
+    );
+  });
+});