diff --git a/sphinx/environment/__init__.py b/sphinx/environment/__init__.py
index 85e2dc9a930..631192b3b74 100644
--- a/sphinx/environment/__init__.py
+++ b/sphinx/environment/__init__.py
@@ -771,7 +771,7 @@ def check_consistency(self) -> None:
         # Call _check_toc_parents here rather than in  _get_toctree_ancestors()
         # because that method is called multiple times per document and would
         # lead to duplicate warnings.
-        _check_toc_parents(self.toctree_includes)
+        _check_toc_parents(self.toctree_includes, self.config.root_doc)
 
         # call check-consistency for all extensions
         self.domains._check_consistency()
@@ -819,19 +819,28 @@ def _traverse_toctree(
                 traversed.add(sub_docname)
 
 
-def _check_toc_parents(toctree_includes: dict[str, list[str]]) -> None:
+def _check_toc_parents(toctree_includes: dict[str, list[str]], root_doc: str) -> None:
+    """Checks if document is referenced in multiple toctrees.
+    Based on the current implementation of `global_toctree_for_doc`,
+    it considers only the descendants of root_doc and not the whole graph.
+    """
     toc_parents: dict[str, list[str]] = {}
-    for parent, children in toctree_includes.items():
-        for child in children:
-            toc_parents.setdefault(child, []).append(parent)
 
+    def _find_toc_parents_dfs(node: str) -> None:
+        for child in toctree_includes.get(node, []):
+            toc_parents.setdefault(child, []).append(node)
+            is_child_already_visited = len(toc_parents[child]) > 1
+            if not is_child_already_visited:
+                _find_toc_parents_dfs(child)
+
+    _find_toc_parents_dfs(root_doc)
     for doc, parents in sorted(toc_parents.items()):
         if len(parents) > 1:
             logger.info(
                 __(
                     'document is referenced in multiple toctrees: %s, selecting: %s <- %s'
                 ),
-                parents,
+                sorted(parents),
                 max(parents),
                 doc,
                 location=doc,
diff --git a/tests/roots/test-toctree-multiple-parents/pdfindex.rst b/tests/roots/test-toctree-multiple-parents/pdfindex.rst
new file mode 100644
index 00000000000..3802732bed3
--- /dev/null
+++ b/tests/roots/test-toctree-multiple-parents/pdfindex.rst
@@ -0,0 +1,7 @@
+test-toctree-multiple-parents
+=============================
+
+.. literalinclude:: relation_graph.txt
+
+.. toctree::
+   delta
diff --git a/tests/roots/test-toctree-multiple-parents/relation_graph.txt b/tests/roots/test-toctree-multiple-parents/relation_graph.txt
index a610eac2622..909de7a9a1e 100644
--- a/tests/roots/test-toctree-multiple-parents/relation_graph.txt
+++ b/tests/roots/test-toctree-multiple-parents/relation_graph.txt
@@ -1,5 +1,5 @@
-     index
-    /     \
+     index   pdfindex
+    /     \  /
  alpha   delta
     \      /
    bravo  /
diff --git a/tests/test_builders/test_build.py b/tests/test_builders/test_build.py
index 5f396cc48af..3b19826a438 100644
--- a/tests/test_builders/test_build.py
+++ b/tests/test_builders/test_build.py
@@ -106,6 +106,9 @@ def test_multiple_parents_toctree(app):
     assert (
         "document is referenced in multiple toctrees: ['bravo', 'delta'], selecting: delta <- charlie"
     ) in app.status.getvalue()
+    assert (
+        "document is referenced in multiple toctrees: ['index', 'pdfindex'], selecting: pdfindex <- delta"
+    ) not in app.status.getvalue()
 
 
 @pytest.mark.usefixtures('_http_teapot')