diff --git a/docker/Dockerfile b/docker/Dockerfile
index cf2cd4c..bc201e1 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -64,7 +64,6 @@ COPY --from=stage_build /emsdk /emsdk
 # This will let use tools offered by this image inside other Docker images
 # (sub-stages) or with custom / no entrypoint
 ENV EMSDK=/emsdk \
-    EM_CONFIG=/emsdk/.emscripten \
     EMSDK_NODE=/emsdk/node/14.18.2_64bit/bin/node \
     PATH="/emsdk:/emsdk/upstream/emscripten:/emsdk/upstream/bin:/emsdk/node/14.18.2_64bit/bin:${PATH}"
 
diff --git a/emsdk.py b/emsdk.py
index 499f14d..c26426b 100644
--- a/emsdk.py
+++ b/emsdk.py
@@ -2676,7 +2676,6 @@ def get_env_vars_to_add(tools_to_activate, system, user):
 
   # A core variable EMSDK points to the root of Emscripten SDK directory.
   env_vars_to_add += [('EMSDK', to_unix_path(emsdk_path()))]
-  env_vars_to_add += [('EM_CONFIG', os.path.normpath(dot_emscripten_path()))]
 
   for tool in tools_to_activate:
     config = tool.activated_config()
@@ -2692,6 +2691,9 @@ def get_env_vars_to_add(tools_to_activate, system, user):
       #   https://github.com/emscripten-core/emscripten/pull/11091
       # - Default to embedded cache also started in 1.39.16
       #   https://github.com/emscripten-core/emscripten/pull/11126
+      # - Emscripten supports automatically locating the embedded
+      #   config in 1.39.13:
+      #   https://github.com/emscripten-core/emscripten/pull/10935
       #
       # Since setting EM_CACHE in the environment effects the entire machine
       # we want to avoid this except when installing these older emscripten
@@ -2700,6 +2702,8 @@ def get_env_vars_to_add(tools_to_activate, system, user):
       if version < [1, 39, 16]:
         em_cache_dir = os.path.join(config['EMSCRIPTEN_ROOT'], 'cache')
         env_vars_to_add += [('EM_CACHE', em_cache_dir)]
+      if version < [1, 39, 13]:
+        env_vars_to_add += [('EM_CONFIG', os.path.normpath(dot_emscripten_path()))]
 
     envs = tool.activated_environment()
     for env in envs:
@@ -2764,7 +2768,7 @@ def construct_env_with_vars(env_vars_to_add):
                      'EMSDK_NUM_CORES', 'EMSDK_NOTTY', 'EMSDK_KEEP_DOWNLOADS'])
   env_keys_to_add = set(pair[0] for pair in env_vars_to_add)
   for key in os.environ:
-    if key.startswith('EMSDK_') or key.startswith('EM_CACHE'):
+    if key.startswith('EMSDK_') or key in ('EM_CACHE', 'EM_CONFIG'):
       if key not in env_keys_to_add and key not in ignore_keys:
         info('Clearing existing environment variable: %s' % key)
         env_string += unset_env(key)
diff --git a/test/test.py b/test/test.py
index deb7240..f9766d0 100755
--- a/test/test.py
+++ b/test/test.py
@@ -10,9 +10,9 @@ import unittest
 WINDOWS = sys.platform.startswith('win')
 MACOS = sys.platform == 'darwin'
 
-assert 'EM_CONFIG' in os.environ, "emsdk should be activated before running this script"
+emconfig = os.path.abspath('.emscripten')
+assert os.path.exists(emconfig)
 
-emconfig = os.environ['EM_CONFIG']
 upstream_emcc = os.path.join('upstream', 'emscripten', 'emcc')
 fastcomp_emcc = os.path.join('fastcomp', 'emscripten', 'emcc')
 emsdk = './emsdk'
diff --git a/test/test_activation.ps1 b/test/test_activation.ps1
index 1aa0a97..6d38ffc 100644
--- a/test/test_activation.ps1
+++ b/test/test_activation.ps1
@@ -28,7 +28,6 @@ try {
     }
 
     $EMSDK = [System.Environment]::GetEnvironmentVariable("EMSDK", $env_type)
-    $EM_CONFIG = [System.Environment]::GetEnvironmentVariable("EM_CONFIG", $env_type)
     $EMSDK_NODE = [System.Environment]::GetEnvironmentVariable("EMSDK_NODE", $env_type)
     $EMSDK_PYTHON = [System.Environment]::GetEnvironmentVariable("EMSDK_PYTHON", $env_type)
     $JAVA_HOME = [System.Environment]::GetEnvironmentVariable("JAVA_HOME", $env_type)
@@ -37,9 +36,6 @@ try {
     if (!$EMSDK) {
         throw "EMSDK is not set for the user"
     }
-    if (!$EM_CONFIG) {
-        throw "EM_CONFIG is not set for the user"
-    }
     if (!$EMSDK_NODE) {
         throw "EMSDK_NODE is not set for the user"
     }
@@ -83,14 +79,12 @@ finally {
 
     # Recover pre activation env variables
     [Environment]::SetEnvironmentVariable("EMSDK", $null, "User")
-    [Environment]::SetEnvironmentVariable("EM_CONFIG", $null, "User")
     [Environment]::SetEnvironmentVariable("EMSDK_NODE", $null, "User")
     [Environment]::SetEnvironmentVariable("EMSDK_PYTHON", $null, "User")
     [Environment]::SetEnvironmentVariable("JAVA_HOME", $null, "User")
 
     try {
         [Environment]::SetEnvironmentVariable("EMSDK", $null, "Machine")
-        [Environment]::SetEnvironmentVariable("EM_CONFIG", $null, "Machine")
         [Environment]::SetEnvironmentVariable("EMSDK_NODE", $null, "Machine")
         [Environment]::SetEnvironmentVariable("EMSDK_PYTHON", $null, "Machine")
         [Environment]::SetEnvironmentVariable("JAVA_HOME", $null, "Machine")
@@ -98,7 +92,6 @@ finally {
 
 
     [Environment]::SetEnvironmentVariable("EMSDK", $null, "Process")
-    [Environment]::SetEnvironmentVariable("EM_CONFIG", $null, "Process")
     [Environment]::SetEnvironmentVariable("EMSDK_NODE", $null, "Process")
     [Environment]::SetEnvironmentVariable("EMSDK_PYTHON", $null, "Process")
     [Environment]::SetEnvironmentVariable("JAVA_HOME", $null, "Process")
diff --git a/test/test_path_preservation.ps1 b/test/test_path_preservation.ps1
index b894954..1547949 100644
--- a/test/test_path_preservation.ps1
+++ b/test/test_path_preservation.ps1
@@ -123,14 +123,12 @@ finally {
 
     # Recover pre activation env variables
     [Environment]::SetEnvironmentVariable("EMSDK", $null, "User")
-    [Environment]::SetEnvironmentVariable("EM_CONFIG", $null, "User")
     [Environment]::SetEnvironmentVariable("EMSDK_NODE", $null, "User")
     [Environment]::SetEnvironmentVariable("EMSDK_PYTHON", $null, "User")
     [Environment]::SetEnvironmentVariable("JAVA_HOME", $null, "User")
 
     try {
         [Environment]::SetEnvironmentVariable("EMSDK", $null, "Machine")
-        [Environment]::SetEnvironmentVariable("EM_CONFIG", $null, "Machine")
         [Environment]::SetEnvironmentVariable("EMSDK_NODE", $null, "Machine")
         [Environment]::SetEnvironmentVariable("EMSDK_PYTHON", $null, "Machine")
         [Environment]::SetEnvironmentVariable("JAVA_HOME", $null, "Machine")
@@ -138,7 +136,6 @@ finally {
 
 
     [Environment]::SetEnvironmentVariable("EMSDK", $null, "Process")
-    [Environment]::SetEnvironmentVariable("EM_CONFIG", $null, "Process")
     [Environment]::SetEnvironmentVariable("EMSDK_NODE", $null, "Process")
     [Environment]::SetEnvironmentVariable("EMSDK_PYTHON", $null, "Process")
     [Environment]::SetEnvironmentVariable("JAVA_HOME", $null, "Process")