diff --git a/esphome/components/store_yaml/__init__.py b/esphome/components/store_yaml/__init__.py
index 733ccd65ef..fa25f36592 100644
--- a/esphome/components/store_yaml/__init__.py
+++ b/esphome/components/store_yaml/__init__.py
@@ -6,7 +6,7 @@ import struct
 
 import esphome.codegen as cg
 import esphome.config_validation as cv
-from esphome.const import CONF_ID, CONF_RAW_DATA_ID
+from esphome.const import CONF_ID, CONF_RAW_DATA_ID, SECRETS_FILES
 from esphome.core import CORE, EsphomeError, HexInt
 
 _LOGGER = logging.getLogger(__name__)
@@ -69,7 +69,10 @@ def _gather_files(include_secrets: bool) -> list[tuple[str, bytes]]:
             continue
         seen.add(resolved)
 
-        is_secret = resolved.name == "secrets.yaml"
+        # Either secrets.yaml or secrets.yml. Symlinks are followed by resolve()
+        # above, so we re-check the original path's name too in case someone
+        # symlinks `secrets.yaml` to a differently-named target.
+        is_secret = resolved.name in SECRETS_FILES or Path(path).name in SECRETS_FILES
         if is_secret and not include_secrets:
             content = REDACTED_PLACEHOLDER
         else:
diff --git a/esphome/config.py b/esphome/config.py
index 5676573d77..a82e41242a 100644
--- a/esphome/config.py
+++ b/esphome/config.py
@@ -1194,8 +1194,11 @@ def _load_config(
     try:
         with yaml_util.track_yaml_loads() as loaded_files:
             config = yaml_util.load_yaml(CORE.config_path)
-        # Stash for components that want the on-disk YAML at codegen time
-        # (e.g. store_yaml embeds them into firmware for recovery).
+            # Resolve deferred !include / package references so the listener
+            # captures every reachable file. Components that want the on-disk
+            # YAML at codegen time (e.g. store_yaml for firmware recovery)
+            # read the list out of CORE.data["yaml_sources"] below.
+            yaml_util.force_load_include_files(config)
         CORE.data["yaml_sources"] = loaded_files
     except EsphomeError as e:
         raise InvalidYAMLError(e) from e