diff --git a/ChangeLog.md b/ChangeLog.md
index ed8db891bb5d6..ebac03e5417cf 100644
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -20,6 +20,8 @@ See docs/process.md for more on how version tagging works.
 
 6.0.1 (in development)
 ----------------------
+- The `-sUSE_PTHREADS` and `-sMEMORY64` flags have been deprecated in favor of the
+  more standard `-pthread` and `-m64` (or `--target=wasm64`) flags. (#27025)
 
 6.0.0 - 06/04/26
 ----------------
diff --git a/site/source/docs/tools_reference/settings_reference.rst b/site/source/docs/tools_reference/settings_reference.rst
index c61cd19e1dc15..ae6a2ab04b7d5 100644
--- a/site/source/docs/tools_reference/settings_reference.rst
+++ b/site/source/docs/tools_reference/settings_reference.rst
@@ -317,6 +317,8 @@ Assumes WASM_BIGINT.
 
 .. note:: Applicable during both linking and compilation
 
+.. note:: This setting is deprecated
+
 Default value: 0
 
 .. _initial_table:
@@ -3393,6 +3395,8 @@ these settings please open a bug (or reply to one of the existing bugs).
  - ``LINKABLE``: under consideration for removal (https://github.com/emscripten-core/emscripten/issues/25262)
  - ``EXPORT_EXCEPTION_HANDLING_HELPERS``: getExceptionMessage is exported anyway when ASSERTIONS or EXCEPTION_STACK_TRACES is set, which are set by default at -O0. At -O1 or above, you can export it separately by -sEXPORTED_RUNTIME_METHODS=getExceptionMessage,decrementExceptionRefcount.
  - ``DETERMINISTIC``: under consideration for removal (https://github.com/emscripten-core/emscripten/issues/26647)
+ - ``USE_PTHREADS``: prefer the standard -pthread flag
+ - ``MEMORY64``: prefer the standard -m64 or --target=wasm64 flags
 
 .. _legacy-settings:
 
diff --git a/src/settings.js b/src/settings.js
index c9e8ad2f6eed5..fa106e281fa76 100644
--- a/src/settings.js
+++ b/src/settings.js
@@ -260,6 +260,7 @@ var MEMORY_GROWTH_LINEAR_STEP = -1;
 // flags, which do the same thing.
 // Assumes WASM_BIGINT.
 // [compile+link]
+// [deprecated]
 var MEMORY64 = 0;
 
 // Sets the initial size of the table when MAIN_MODULE or SIDE_MODULE is used
diff --git a/test/test_other.py b/test/test_other.py
index 029dfd7857d2b..ea4d59c7a4979 100644
--- a/test/test_other.py
+++ b/test/test_other.py
@@ -14005,7 +14005,7 @@ def test_USE_PTHREADS(self):
     self.set_setting('USE_PTHREADS')
     self.set_setting('PROXY_TO_PTHREAD')
     self.set_setting('EXIT_RUNTIME')
-    self.do_runf('pthread/test_pthread_create.c')
+    self.do_runf('pthread/test_pthread_create.c', cflags=['-Wno-deprecated'])
 
   def test_cpp_module(self):
     self.run_process([EMXX, '-std=c++20', test_file('other/hello_world.cppm'), '--precompile', '-o', 'hello_world.pcm'])
@@ -15356,3 +15356,10 @@ def test_logReadFiles(self):
     create_file('pre.js', 'Module.logReadFiles = 1;')
     output = self.do_runf('checksummer.c', args=['test.txt'], cflags=['--pre-js=pre.js'])
     self.assertContained('read file: /test.txt', output)
+
+  def test_deprecated_settings(self):
+    err = self.run_process([EMCC, '-sMEMORY64', test_file('hello_world.c')], stderr=PIPE).stderr
+    self.assertContained('emcc: warning: MEMORY64 is deprecated (prefer the standard -m64 or --target=wasm64 flags). Please open a bug if you have a continuing need for this setting [-Wdeprecated]', err)
+
+    err = self.run_process([EMCC, '-sUSE_PTHREADS', test_file('hello_world.c')], stderr=PIPE).stderr
+    self.assertContained('emcc: warning: USE_PTHREADS is deprecated (prefer the standard -pthread flag). Please open a bug if you have a continuing need for this setting [-Wdeprecated]', err)
diff --git a/tools/link.py b/tools/link.py
index b4a575fe1ec30..f2f7b97850685 100644
--- a/tools/link.py
+++ b/tools/link.py
@@ -634,6 +634,9 @@ def add_system_js_lib(lib):
 def check_settings():
   for s, reason in DEPRECATED_SETTINGS.items():
     if s in user_settings:
+      if s == 'MEMORY64' and user_settings[s] == '2':
+        # Don't warn about -sMEMORY64=2 (since its the only way to enable the lowering pass)
+        continue
       diagnostics.warning('deprecated', f'{s} is deprecated ({reason}). Please open a bug if you have a continuing need for this setting')
 
   for name, msg in EXPERIMENTAL_SETTINGS.items():
diff --git a/tools/settings.py b/tools/settings.py
index 8a682e85e9a48..87e1e65581d65 100644
--- a/tools/settings.py
+++ b/tools/settings.py
@@ -115,6 +115,8 @@
     'LINKABLE': 'under consideration for removal (https://github.com/emscripten-core/emscripten/issues/25262)',
     'EXPORT_EXCEPTION_HANDLING_HELPERS': 'getExceptionMessage is exported anyway when ASSERTIONS or EXCEPTION_STACK_TRACES is set, which are set by default at -O0. At -O1 or above, you can export it separately by -sEXPORTED_RUNTIME_METHODS=getExceptionMessage,decrementExceptionRefcount.',
     'DETERMINISTIC': 'under consideration for removal (https://github.com/emscripten-core/emscripten/issues/26647)',
+    'USE_PTHREADS': 'prefer the standard -pthread flag',
+    'MEMORY64': 'prefer the standard -m64 or --target=wasm64 flags',
 }
 
 # Settings that don't need to be externalized when serializing to json because they