diff --git a/site/source/docs/tools_reference/settings_reference.rst b/site/source/docs/tools_reference/settings_reference.rst
index 556d4d267ae83..44b015ecfba11 100644
--- a/site/source/docs/tools_reference/settings_reference.rst
+++ b/site/source/docs/tools_reference/settings_reference.rst
@@ -469,6 +469,8 @@ emulated values may not match (this is true of native too, for that matter -
 this is all undefined behavior). This approaches appears good enough to
 support Python, which is the main use case motivating this feature.
 
+.. note:: This setting is deprecated
+
 Default value: false
 
 .. _exception_debug:
@@ -3096,6 +3098,8 @@ normal wasm or that wasm2js code. For details of how to do that, see the
 test_maybe_wasm2js test.  This option can be useful for debugging and
 bisecting.
 
+.. note:: This setting is deprecated
+
 Default value: false
 
 .. _asan_shadow_size:
diff --git a/src/settings.js b/src/settings.js
index 5a864eaf13e49..ad09a1a3cb837 100644
--- a/src/settings.js
+++ b/src/settings.js
@@ -344,6 +344,7 @@ var SAFE_HEAP_LOG = false;
 // this is all undefined behavior). This approaches appears good enough to
 // support Python, which is the main use case motivating this feature.
 // [link]
+// [deprecated]
 var EMULATE_FUNCTION_POINTER_CASTS = false;
 
 // Print out exceptions in emscriptened code.
@@ -2027,6 +2028,7 @@ var MINIFY_HTML = true;
 // test_maybe_wasm2js test.  This option can be useful for debugging and
 // bisecting.
 // [link]
+// [deprecated]
 var MAYBE_WASM2JS = false;
 
 // This option is no longer used. The appropriate shadow memory size is now
diff --git a/tools/settings.py b/tools/settings.py
index b1498637fedbd..c10192d4b58d8 100644
--- a/tools/settings.py
+++ b/tools/settings.py
@@ -117,6 +117,8 @@
 #
 # At some point in the future, once folks have stopped using these
 # settings we can move them to `LEGACY_SETTINGS`.
+#
+# All settings here should be tagged as `[deprecated]` in settings.js
 DEPRECATED_SETTINGS = {
     'SUPPORT_ERRNO': 'emscripten no longer uses the setErrNo library function',
     'EXTRA_EXPORTED_RUNTIME_METHODS': 'please use EXPORTED_RUNTIME_METHODS instead',