diff --git a/.serena/project.yml b/.serena/project.yml
index 62e6c5c8..004546bd 100644
--- a/.serena/project.yml
+++ b/.serena/project.yml
@@ -146,3 +146,7 @@ language_backend:
 # list of regex patterns which, when matched, mark a memory entry as read‑only.
 # Extends the list from the global configuration, merging the two lists.
 read_only_memory_patterns: []
+
+# line ending convention for file writes: unset (use global setting, "lf", "crlf", or "native" (platform default)
+# If not undefined, overrides the global setting in serena_config.yml
+line_ending:
diff --git a/src/serena/config/serena_config.py b/src/serena/config/serena_config.py
index 7daf3922..d8e10a65 100644
--- a/src/serena/config/serena_config.py
+++ b/src/serena/config/serena_config.py
@@ -591,11 +591,6 @@ class SerenaConfig(SharedConfig):
     jetbrains_plugin_server_address: str = "127.0.0.1"
     tool_timeout: float = DEFAULT_TOOL_TIMEOUT
 
-    language_backend: LanguageBackend = LanguageBackend.LSP
-    """
-    the language backend to use for code understanding features
-    """
-
     token_count_estimator: str = RegisteredTokenCountEstimator.CHAR_COUNT.name
     """Only relevant if `record_tool_usage` is True; the name of the token count estimator to use for tool usage statistics.
     See the `RegisteredTokenCountEstimator` enum for available options.
@@ -628,9 +623,13 @@ class SerenaConfig(SharedConfig):
     """
 
     # settings with overridden defaults
+    language_backend: LanguageBackend = LanguageBackend.LSP
+    """
+    the language backend to use for code understanding features
+    """
     default_modes: Sequence[str] | None = ("interactive", "editing")
-    symbol_info_budget: float = 10.0
     line_ending: LineEnding = LineEnding.NATIVE
+    symbol_info_budget: float = 10.0
     """
     Time budget (seconds) for requests when tools request include_info (currently
     only supported for LSP-based tools).
@@ -783,11 +782,12 @@ class SerenaConfig(SharedConfig):
         instance.language_backend = language_backend
 
         # determine line ending
-        line_ending = get_dataclass_default(SerenaConfig, "line_ending")
         line_ending_value = loaded_commented_yaml.get("line_ending")
         if line_ending_value:
-            line_ending = LineEnding.from_str(line_ending_value)
-        instance.line_ending = line_ending
+            instance.line_ending = LineEnding.from_str(line_ending_value)
+        else:
+            num_migrations += 1
+            instance.line_ending = get_dataclass_default(SerenaConfig, "line_ending")
 
         # migrate deprecated "gui_log_level" field if necessary
         if "gui_log_level" in loaded_commented_yaml:
diff --git a/src/serena/resources/project.template.yml b/src/serena/resources/project.template.yml
index 5273b5b6..b5b55d86 100644
--- a/src/serena/resources/project.template.yml
+++ b/src/serena/resources/project.template.yml
@@ -31,8 +31,10 @@ languages: ["python"]
 # For a list of possible encodings, see https://docs.python.org/3.11/library/codecs.html#standard-encodings
 encoding: "utf-8"
 
-# line ending convention for file writes: "lf", "crlf", or "native" (platform default)
-line_ending: "native"
+# line ending convention to use when writing source files.
+# Possible values: unset (use global setting), "lf", "crlf", or "native" (platform default)
+# This does not affect Serena's own files (e.g. memories and configuration files), which always use native line endings.
+line_ending:
 
 # The language backend to use for this project.
 # If not set, the global setting from serena_config.yml is used.
diff --git a/src/serena/resources/serena_config.template.yml b/src/serena/resources/serena_config.template.yml
index cc3f3ffd..0c4a6d38 100644
--- a/src/serena/resources/serena_config.template.yml
+++ b/src/serena/resources/serena_config.template.yml
@@ -7,9 +7,10 @@
 #      in your IDE).
 language_backend: LSP
 
-# line ending convention for file writes across all projects.
+# line ending convention to use when writing source files.
 # Possible values: "lf" (Unix), "crlf" (Windows), "native" (platform default).
-# Can be overridden per project in project.yml.
+# Note that Serena's own files (e.g. memories and configuration files) always use native line endings.
+# This setting can be overridden on a per-project basis in project.yml files.
 line_ending: native
 
 # whether to open a graphical window with Serena's logs.