diff --git a/esphome/components/store_yaml/__init__.py b/esphome/components/store_yaml/__init__.py
index d9d3052ebd4..d950465d5d6 100644
--- a/esphome/components/store_yaml/__init__.py
+++ b/esphome/components/store_yaml/__init__.py
@@ -197,6 +197,22 @@ def _collect_sensitive_values() -> dict[str, _SensitiveValue]:
     return result
 
 
+# Envelope path of the note recording includes that could not be captured.
+UNCAPTURED_NOTE_PATH = "store_yaml_uncaptured.yaml"
+
+
+def _uncaptured_note(unresolved: list[str]) -> tuple[str, bytes]:
+    """Comment-only YAML entry listing includes that could not be captured, so
+    a recovered config never silently appears complete. Emitted for both the
+    redacted and verbatim paths; user files are never modified to carry it."""
+    text = (
+        "# store_yaml: the following !include paths use substitutions and\n"
+        "# could not be captured; restore these files manually:\n"
+        + "".join(f"#   {inc}\n" for inc in unresolved)
+    )
+    return (UNCAPTURED_NOTE_PATH, text.encode("utf-8"))
+
+
 def _build_secrets_skeleton(keys: set[str]) -> bytes:
     parts = [SECRETS_SKELETON_HEADER]
     parts.extend(f'{key}: ""\n' for key in sorted(keys))
@@ -204,7 +220,7 @@ def _build_secrets_skeleton(keys: set[str]) -> bytes:
 
 
 def _generate_redacted_files(
-    entries: list[tuple[str, Path]], secret_rels: set[str], unresolved: list[str]
+    entries: list[tuple[str, Path]], secret_rels: set[str]
 ) -> list[tuple[str, bytes]]:
     """Re-generate each captured file from its parse tree with cv.sensitive
     values emitted as `!secret <name>` references, and replace secrets files
@@ -248,19 +264,6 @@ def _generate_redacted_files(
             "embed secrets deliberately."
         )
 
-    if unresolved:
-        # Record the gap inside the recovered config itself, not just in a
-        # compile-time log line: substitution-pathed includes can't be
-        # captured, so the user must restore those files manually.
-        # Discovery parses the entry file first, so entries[0] is the entry.
-        entry_rel = entries[0][0]
-        texts[entry_rel] = (
-            "# store_yaml: the following !include paths use substitutions and\n"
-            "# could not be captured; restore these files manually:\n"
-            + "".join(f"#   {inc}\n" for inc in unresolved)
-            + texts[entry_rel]
-        )
-
     skeleton = _build_secrets_skeleton(skeleton_keys)
     result = [
         (rel, skeleton if rel in secret_rels else texts[rel].encode("utf-8"))
@@ -337,7 +340,9 @@ async def to_code(config: ConfigType) -> None:
     if config[CONF_INCLUDE_SECRETS]:
         files = _read_files_verbatim(entries)
     else:
-        files = _generate_redacted_files(entries, secret_rels, discovered.unresolved)
+        files = _generate_redacted_files(entries, secret_rels)
+    if discovered.unresolved:
+        files.append(_uncaptured_note(discovered.unresolved))
     envelope = _pack_envelope(files)
     compressed = zstd.compress(envelope, level=ZSTD_LEVEL)
 
diff --git a/tests/unit_tests/components/test_store_yaml.py b/tests/unit_tests/components/test_store_yaml.py
index 906ed32f078..95e5b182dee 100644
--- a/tests/unit_tests/components/test_store_yaml.py
+++ b/tests/unit_tests/components/test_store_yaml.py
@@ -10,10 +10,12 @@ import pytest
 from esphome import yaml_util
 from esphome.components.store_yaml import (
     SECRETS_SKELETON_HEADER,
+    UNCAPTURED_NOTE_PATH,
     _gather_files,
     _generate_redacted_files,
     _pack_envelope,
     _read_files_verbatim,
+    _uncaptured_note,
     unpack_envelope,
 )
 from esphome.core import CORE, EsphomeError
@@ -49,7 +51,7 @@ def _sources(
 
 def _gather_redacted(discovered: DiscoveredYamlFiles) -> dict[str, bytes]:
     entries, secret_rels = _gather_files(discovered)
-    return dict(_generate_redacted_files(entries, secret_rels, discovered.unresolved))
+    return dict(_generate_redacted_files(entries, secret_rels))
 
 
 # ---------------------------------------------------------------------------
@@ -272,14 +274,13 @@ def test_redacted_accepts_secret_only_values(project: Path) -> None:
     assert 'api_key: ""' in files["secrets.yaml"].decode()
 
 
-def test_redacted_records_unresolved_includes_in_entry_file(project: Path) -> None:
-    """Substitution-pathed includes that can't be captured are noted inside the
-    recovered entry file, not just in a compile-time log line."""
-    discovered = _sources(project, "entry.yaml", "secrets.yaml")
-    discovered.unresolved.append("${board}.yaml")
-    files = _gather_redacted(discovered)
-    text = files["entry.yaml"].decode()
-    assert text.startswith("# store_yaml: the following !include paths")
+def test_uncaptured_note_lists_missing_includes() -> None:
+    """Substitution-pathed includes that can't be captured are recorded in a
+    dedicated envelope entry (both modes), not just a compile-time log line."""
+    rel, content = _uncaptured_note(["${board}.yaml"])
+    assert rel == UNCAPTURED_NOTE_PATH
+    text = content.decode()
+    assert text.startswith("# store_yaml:")
     assert "#   ${board}.yaml" in text