diff --git a/graphify/extract.py b/graphify/extract.py
index 4b9efa732..f7ac9864e 100644
--- a/graphify/extract.py
+++ b/graphify/extract.py
@@ -6950,7 +6950,9 @@ def _extract_single_file(args: tuple) -> tuple[int, dict]:
     # (e.g. a transient batch/parallel hiccup). Caching it makes the empty
     # byte-stable across runs and silently blinds affected/explain to and
     # through the file (#1666); skipping the write lets a rerun self-heal.
-    if not bypass_cache and "error" not in result and result.get("nodes"):
+    # An intentional decline or virtual workspace root (result.get("skipped"))
+    # is cached so repeat runs do not re-extract and re-report it (#3910).
+    if not bypass_cache and "error" not in result and (result.get("nodes") or result.get("skipped")):
         save_cached(path, result, root, cache_root=cache_location)
     return idx, result
 
@@ -7152,8 +7154,9 @@ def _extract_sequential(
         bypass_cache = path.suffix in _JS_CACHE_BYPASS_SUFFIXES
         # XAML boundary anchors on `root` (the corpus), not the cache location.
         result = _safe_extract_with_xaml_root(extractor, path, root)
-        # See _extract_single_file: don't cache an anomalous zero-node result (#1666).
-        if not bypass_cache and "error" not in result and result.get("nodes"):
+        # See _extract_single_file: don't cache an anomalous zero-node result (#1666),
+        # but cache intentional declines/virtual manifests carrying `skipped` (#3910).
+        if not bypass_cache and "error" not in result and (result.get("nodes") or result.get("skipped")):
             save_cached(path, result, root, cache_root=cache_location)
         per_file[idx] = result
     if total_files >= _PROGRESS_INTERVAL:
diff --git a/graphify/manifest_ingest.py b/graphify/manifest_ingest.py
index a36071930..bffb7bc3b 100644
--- a/graphify/manifest_ingest.py
+++ b/graphify/manifest_ingest.py
@@ -91,6 +91,8 @@ def extract_package_manifest(path: Path) -> dict[str, Any]:
         info = _PARSERS[eco](text)
     except Exception as exc:  # noqa: BLE001 — a malformed manifest must not abort extraction
         return {"nodes": [], "edges": [], "error": f"manifest parse error: {exc}"}
+    if isinstance(info, dict) and info.get("skipped"):
+        return {"nodes": [], "edges": [], "skipped": info["skipped"]}
     if not info or not info.get("name"):
         return {"nodes": [], "edges": []}
 
@@ -237,6 +239,8 @@ def _parse_cargo(text: str) -> dict | None:
     # package of its own — emit nothing rather than a fabricated node. ``name`` is
     # never workspace-inheritable in Cargo, but guard on the type anyway.
     if not isinstance(name, str) or not name:
+        if isinstance(data.get("workspace"), dict):
+            return {"name": None, "skipped": "virtual workspace root Cargo.toml"}
         return None
     # ``version`` may be workspace-inherited (``version.workspace = true``), which
     # parses to a table; keep only a concrete string version.
diff --git a/tests/test_manifest_ingest.py b/tests/test_manifest_ingest.py
index 6407e477b..5ddd85583 100644
--- a/tests/test_manifest_ingest.py
+++ b/tests/test_manifest_ingest.py
@@ -136,12 +136,26 @@ def test_cargo_parses_name_version_and_deps(tmp_path):
     assert {"pkg_serde", "pkg_tokio"} <= deps  # inline-table dep keyed by name
 
 
-def test_cargo_virtual_workspace_manifest_emits_no_package(tmp_path):
+def test_cargo_virtual_workspace_manifest_emits_no_package(tmp_path, capsys):
     # A virtual workspace root has no [package] table, so it declares no package
-    # of its own — it must not fabricate a node.
+    # of its own — it must not fabricate a node, and is skipped by design (#3910).
     p = _write(tmp_path / "Cargo.toml", '[workspace]\nmembers = ["a", "b"]\n')
     r = extract_package_manifest(p)
     assert _pkg_nodes(r) == []
+    assert r.get("skipped") == "virtual workspace root Cargo.toml"
+
+    # In extract(): must not emit zero-node warning, must not be marked failed, and must be cached
+    result = extract([p], cache_root=tmp_path)
+    err = capsys.readouterr().err
+    assert "zero nodes" not in err
+    assert result.get("failed_sources") == []
+
+    # Caching verification: load_cached returns the skipped result
+    from graphify.cache import load_cached
+    cached = load_cached(p, tmp_path, cache_root=tmp_path)
+    assert cached is not None
+    assert cached.get("skipped") == "virtual workspace root Cargo.toml"
+    assert cached.get("nodes") == []
 
 
 def test_cargo_target_conditional_deps_are_collected(tmp_path):