diff --git a/src/apm_cli/commands/audit.py b/src/apm_cli/commands/audit.py
index c701f1826..053a21e61 100644
--- a/src/apm_cli/commands/audit.py
+++ b/src/apm_cli/commands/audit.py
@@ -436,7 +436,7 @@ def _audit_ci_gate(
     fail_fast = not no_fail_fast
 
     # Always run baseline checks
-    ci_result = run_baseline_checks(cfg.project_root, fail_fast=fail_fast)
+    ci_result = run_baseline_checks(cfg.project_root, fail_fast=fail_fast, ci_mode=True)
 
     # Resolve policy source: explicit --policy wins; otherwise mirror
     # install's auto-discovery (closes #827) so CI catches sideloaded
diff --git a/src/apm_cli/policy/ci_checks.py b/src/apm_cli/policy/ci_checks.py
index 7b2ab1222..d71f69a53 100644
--- a/src/apm_cli/policy/ci_checks.py
+++ b/src/apm_cli/policy/ci_checks.py
@@ -16,7 +16,7 @@
 from pathlib import Path
 from typing import TYPE_CHECKING, List, Optional, Sequence  # noqa: F401, UP035
 
-from ..deps.lockfile import _SELF_KEY
+from ..deps.lockfile import _SELF_KEY, LEGACY_LOCKFILE_NAME, LOCKFILE_NAME
 from .models import CheckResult, CIAuditResult
 
 if TYPE_CHECKING:
@@ -503,11 +503,14 @@ def run_baseline_checks(
     project_root: Path,
     *,
     fail_fast: bool = True,
+    ci_mode: bool = False,
 ) -> CIAuditResult:
     """Run all baseline CI checks against a project directory.
 
     When *fail_fast* is ``True`` (default), stops after the first
     failing check to skip expensive I/O (e.g. content integrity scan).
+    When *ci_mode* is ``True``, the ``manifest-missing`` check is a hard
+    failure (``passed=False``); otherwise it is an advisory warning only.
     Returns :class:`CIAuditResult` with individual check results.
     """
     from ..deps.lockfile import LockFile, get_lockfile_path
@@ -545,8 +548,25 @@ def run_baseline_checks(
     lockfile_path = get_lockfile_path(project_root)
 
     # If there's no apm.yml or no lockfile, the first check already passed
-    # (no deps needed).  Skip remaining checks.
+    # (no deps needed).  Skip remaining checks -- but warn if APM artifacts
+    # exist without a manifest (evidence of a deleted apm.yml).
     if not apm_yml_path.exists() or not lockfile_path.exists():
+        if not apm_yml_path.exists():
+            apm_dir = project_root / ".apm"
+            lock_file = project_root / LOCKFILE_NAME
+            legacy_lock_file = project_root / LEGACY_LOCKFILE_NAME
+            if apm_dir.is_dir() or lock_file.exists() or legacy_lock_file.exists():
+                result.checks.append(
+                    CheckResult(
+                        name="manifest-missing",
+                        passed=not ci_mode,
+                        message=(
+                            "apm.yml is missing but APM artifacts"
+                            " (.apm/ or apm.lock.yaml or apm.lock) were found"
+                            " -- this may indicate a deleted manifest"
+                        ),
+                    )
+                )
         return result
 
     lock = LockFile.read(lockfile_path)
diff --git a/src/apm_cli/policy/models.py b/src/apm_cli/policy/models.py
index 5ee31aae4..a0d6cc880 100644
--- a/src/apm_cli/policy/models.py
+++ b/src/apm_cli/policy/models.py
@@ -34,6 +34,7 @@
     "scripts-policy": "apm.yml",
     "unmanaged-files": "apm.yml",
     "manifest-parse": "apm.yml",
+    "manifest-missing": "apm.yml",
 }
 
 
diff --git a/tests/unit/policy/test_ci_checks.py b/tests/unit/policy/test_ci_checks.py
index 0dacfaede..4e885f950 100644
--- a/tests/unit/policy/test_ci_checks.py
+++ b/tests/unit/policy/test_ci_checks.py
@@ -1119,3 +1119,80 @@ def test_remediation_hint_present_in_error_message(self, tmp_path: Path) -> None
         assert parse_check.name == "manifest-parse"
         assert "Cannot parse apm.yml" in parse_check.message
         assert "fix the YAML syntax error in apm.yml and re-run" in parse_check.message
+
+
+class TestManifestMissingWarning:
+    """Tests for the manifest-missing warning when apm.yml is absent."""
+
+    def test_no_artifacts_no_warning(self, tmp_path: Path) -> None:
+        """Clean non-APM project: no apm.yml, no .apm/, no lockfile -> no warning."""
+        result = run_baseline_checks(tmp_path)
+        names = [c.name for c in result.checks]
+        assert "manifest-missing" not in names
+        assert result.passed
+
+    def test_apm_dir_triggers_warning(self, tmp_path: Path) -> None:
+        """apm.yml absent but .apm/ dir exists -> manifest-missing warning."""
+        (tmp_path / ".apm").mkdir()
+        result = run_baseline_checks(tmp_path)
+        names = [c.name for c in result.checks]
+        assert "manifest-missing" in names
+        check = next(c for c in result.checks if c.name == "manifest-missing")
+        assert check.passed is True
+        assert ".apm/" in check.message or "apm.lock.yaml" in check.message
+
+    def test_lockfile_triggers_warning(self, tmp_path: Path) -> None:
+        """apm.yml absent but apm.lock.yaml exists -> manifest-missing warning."""
+        (tmp_path / "apm.lock.yaml").write_text("packages: []\n", encoding="utf-8")
+        result = run_baseline_checks(tmp_path)
+        names = [c.name for c in result.checks]
+        assert "manifest-missing" in names
+        check = next(c for c in result.checks if c.name == "manifest-missing")
+        assert check.passed is True
+
+    def test_manifest_present_no_warning(self, tmp_path: Path) -> None:
+        """apm.yml present -> no manifest-missing check at all."""
+        _write_apm_yml(tmp_path)
+        result = run_baseline_checks(tmp_path)
+        names = [c.name for c in result.checks]
+        assert "manifest-missing" not in names
+
+    def test_apm_dir_ci_mode_fails(self, tmp_path: Path) -> None:
+        """In CI mode, .apm/ without apm.yml fails the check."""
+        (tmp_path / ".apm").mkdir()
+        result = run_baseline_checks(tmp_path, ci_mode=True)
+        check = next(c for c in result.checks if c.name == "manifest-missing")
+        assert check.passed is False
+        assert not result.passed
+
+    def test_lockfile_ci_mode_fails(self, tmp_path: Path) -> None:
+        """In CI mode, apm.lock.yaml without apm.yml fails the check."""
+        (tmp_path / "apm.lock.yaml").write_text("packages: []\n", encoding="utf-8")
+        result = run_baseline_checks(tmp_path, ci_mode=True)
+        check = next(c for c in result.checks if c.name == "manifest-missing")
+        assert check.passed is False
+        assert not result.passed
+
+    def test_legacy_lockfile_triggers_warning(self, tmp_path: Path) -> None:
+        """apm.yml absent but legacy apm.lock exists -> manifest-missing warning."""
+        (tmp_path / "apm.lock").write_text("packages: []\n", encoding="utf-8")
+        result = run_baseline_checks(tmp_path)
+        names = [c.name for c in result.checks]
+        assert "manifest-missing" in names
+        check = next(c for c in result.checks if c.name == "manifest-missing")
+        assert check.passed is True
+
+    def test_legacy_lockfile_ci_mode_fails(self, tmp_path: Path) -> None:
+        """In CI mode, legacy apm.lock without apm.yml fails the check."""
+        (tmp_path / "apm.lock").write_text("packages: []\n", encoding="utf-8")
+        result = run_baseline_checks(tmp_path, ci_mode=True)
+        check = next(c for c in result.checks if c.name == "manifest-missing")
+        assert check.passed is False
+        assert not result.passed
+
+    def test_no_artifacts_ci_mode_still_passes(self, tmp_path: Path) -> None:
+        """Clean project with no APM artifacts passes even in CI mode."""
+        result = run_baseline_checks(tmp_path, ci_mode=True)
+        names = [c.name for c in result.checks]
+        assert "manifest-missing" not in names
+        assert result.passed