diff --git a/ChangeLog.md b/ChangeLog.md
index 0b001a962adab..74590949c67e2 100644
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -20,6 +20,10 @@ See docs/process.md for more on how version tagging works.
 
 4.0.21 (in development)
 -----------------------
+- The emscripten tools will now warn if they are not run via the launcher
+  scripts.  i.e. it is no longer officially supported to run `python emcc.py`.
+  Instead, `emcc` should be run directly (via the provided `.bat` or shell
+  script). (#20437)
 - The `-sPROXY_TO_WORKER` setting (along with the corresponding
   `--proxy-to-worker` flag) was removed due to lack of usage.  If you were
   depending on this feature but missed the PSA, please let us know about your
diff --git a/bootstrap b/bootstrap
index 26334343d9eaa..782bfa2e1132f 100755
--- a/bootstrap
+++ b/bootstrap
@@ -30,4 +30,5 @@ if [ -z "$_EM_PY" ]; then
   exit 1
 fi
 
+export _EM_LAUNCHER=1
 exec "$_EM_PY" -E "$0.py" "$@"
diff --git a/bootstrap.bat b/bootstrap.bat
index e9080623b77f0..e370c8b30c51f 100644
--- a/bootstrap.bat
+++ b/bootstrap.bat
@@ -10,6 +10,9 @@
 
 :: All env. vars specified in this file are to be local only to this script.
 @setlocal
+
+@set _EM_LAUNCHER=1
+
 :: -E will not ignore _PYTHON_SYSCONFIGDATA_NAME an internal
 :: of cpython used in cross compilation via setup.py.
 @set _PYTHON_SYSCONFIGDATA_NAME=
diff --git a/em++ b/em++
index bdbda2fbb9244..c0d052e945a15 100755
--- a/em++
+++ b/em++
@@ -30,6 +30,7 @@ if [ -z "$_EM_PY" ]; then
   exit 1
 fi
 
+export _EM_LAUNCHER=1
 if [ -z "$_EMCC_CCACHE" ]; then
   exec "$_EM_PY" -E "$0.py" "$@"
 else
diff --git a/em++.bat b/em++.bat
index dd5aa6565a35b..82ca72491b085 100644
--- a/em++.bat
+++ b/em++.bat
@@ -10,9 +10,13 @@
 
 :: All env. vars specified in this file are to be local only to this script.
 @setlocal
+
+@set _EM_LAUNCHER=1
+
 :: -E will not ignore _PYTHON_SYSCONFIGDATA_NAME an internal
 :: of cpython used in cross compilation via setup.py.
 @set _PYTHON_SYSCONFIGDATA_NAME=
+
 @set _EM_PY=%EMSDK_PYTHON%
 @if "%_EM_PY%"=="" (
   set _EM_PY=python
diff --git a/emcc b/emcc
index bdbda2fbb9244..c0d052e945a15 100755
--- a/emcc
+++ b/emcc
@@ -30,6 +30,7 @@ if [ -z "$_EM_PY" ]; then
   exit 1
 fi
 
+export _EM_LAUNCHER=1
 if [ -z "$_EMCC_CCACHE" ]; then
   exec "$_EM_PY" -E "$0.py" "$@"
 else
diff --git a/emcc.bat b/emcc.bat
index dd5aa6565a35b..82ca72491b085 100644
--- a/emcc.bat
+++ b/emcc.bat
@@ -10,9 +10,13 @@
 
 :: All env. vars specified in this file are to be local only to this script.
 @setlocal
+
+@set _EM_LAUNCHER=1
+
 :: -E will not ignore _PYTHON_SYSCONFIGDATA_NAME an internal
 :: of cpython used in cross compilation via setup.py.
 @set _PYTHON_SYSCONFIGDATA_NAME=
+
 @set _EM_PY=%EMSDK_PYTHON%
 @if "%_EM_PY%"=="" (
   set _EM_PY=python
diff --git a/test/runner b/test/runner
index 26334343d9eaa..782bfa2e1132f 100755
--- a/test/runner
+++ b/test/runner
@@ -30,4 +30,5 @@ if [ -z "$_EM_PY" ]; then
   exit 1
 fi
 
+export _EM_LAUNCHER=1
 exec "$_EM_PY" -E "$0.py" "$@"
diff --git a/test/runner.bat b/test/runner.bat
index e9080623b77f0..e370c8b30c51f 100644
--- a/test/runner.bat
+++ b/test/runner.bat
@@ -10,6 +10,9 @@
 
 :: All env. vars specified in this file are to be local only to this script.
 @setlocal
+
+@set _EM_LAUNCHER=1
+
 :: -E will not ignore _PYTHON_SYSCONFIGDATA_NAME an internal
 :: of cpython used in cross compilation via setup.py.
 @set _PYTHON_SYSCONFIGDATA_NAME=
diff --git a/test/test_other.py b/test/test_other.py
index deed55ef59e96..c35345ce48000 100644
--- a/test/test_other.py
+++ b/test/test_other.py
@@ -15210,3 +15210,7 @@ def test_binary_encode(self):
 console.log('OK');'''
     write_file('test.js', read_file(path_from_root('src/binaryDecode.js')) + '\nvar src = ' + binary_encoded + ';\n' + test_js)
     self.assertContained('OK', self.run_js('test.js'))
+
+  def test_direct_usage_warning(self):
+    err = self.run_process([sys.executable, path_from_root('emcc.py'), '--version'], stderr=PIPE).stderr
+    self.assertContained('emcc: warning: python script (`emcc.py`) was run directly rather than run via launcher', err)
diff --git a/tools/maint/run_python.bat b/tools/maint/run_python.bat
index e9080623b77f0..e370c8b30c51f 100644
--- a/tools/maint/run_python.bat
+++ b/tools/maint/run_python.bat
@@ -10,6 +10,9 @@
 
 :: All env. vars specified in this file are to be local only to this script.
 @setlocal
+
+@set _EM_LAUNCHER=1
+
 :: -E will not ignore _PYTHON_SYSCONFIGDATA_NAME an internal
 :: of cpython used in cross compilation via setup.py.
 @set _PYTHON_SYSCONFIGDATA_NAME=
diff --git a/tools/maint/run_python.sh b/tools/maint/run_python.sh
index 26334343d9eaa..782bfa2e1132f 100755
--- a/tools/maint/run_python.sh
+++ b/tools/maint/run_python.sh
@@ -30,4 +30,5 @@ if [ -z "$_EM_PY" ]; then
   exit 1
 fi
 
+export _EM_LAUNCHER=1
 exec "$_EM_PY" -E "$0.py" "$@"
diff --git a/tools/maint/run_python_compiler.bat b/tools/maint/run_python_compiler.bat
index dd5aa6565a35b..82ca72491b085 100644
--- a/tools/maint/run_python_compiler.bat
+++ b/tools/maint/run_python_compiler.bat
@@ -10,9 +10,13 @@
 
 :: All env. vars specified in this file are to be local only to this script.
 @setlocal
+
+@set _EM_LAUNCHER=1
+
 :: -E will not ignore _PYTHON_SYSCONFIGDATA_NAME an internal
 :: of cpython used in cross compilation via setup.py.
 @set _PYTHON_SYSCONFIGDATA_NAME=
+
 @set _EM_PY=%EMSDK_PYTHON%
 @if "%_EM_PY%"=="" (
   set _EM_PY=python
diff --git a/tools/maint/run_python_compiler.sh b/tools/maint/run_python_compiler.sh
index bdbda2fbb9244..c0d052e945a15 100644
--- a/tools/maint/run_python_compiler.sh
+++ b/tools/maint/run_python_compiler.sh
@@ -30,6 +30,7 @@ if [ -z "$_EM_PY" ]; then
   exit 1
 fi
 
+export _EM_LAUNCHER=1
 if [ -z "$_EMCC_CCACHE" ]; then
   exec "$_EM_PY" -E "$0.py" "$@"
 else
diff --git a/tools/shared.py b/tools/shared.py
index a51ca7974e26c..221df62f61f14 100644
--- a/tools/shared.py
+++ b/tools/shared.py
@@ -620,6 +620,13 @@ def get_llvm_target():
 def init():
   utils.set_version_globals()
   setup_temp_dirs()
+  if '_EM_LAUNCHER' not in os.environ:
+    actual = bat_suffix(os.path.basename(sys.argv[0]))
+    launcher = os.path.splitext(actual)[0]
+    diagnostics.warning('unsupported', f'python script (`{actual}`) was run directly rather than run via launcher.  Running via `{launcher}` is recommended')
+  else:
+    # We don't want subprocesses to inherit this environment variable.
+    del os.environ['_EM_LAUNCHER']
 
 
 # ============================================================================