diff --git a/debug_toolbar/apps.py b/debug_toolbar/apps.py
index de469f190..2848e72d5 100644
--- a/debug_toolbar/apps.py
+++ b/debug_toolbar/apps.py
@@ -22,6 +22,24 @@ def ready(self):
         DebugToolbar.get_panel_classes()
 
 
+def check_template_config(config):
+    """
+    Checks if a template configuration is valid.
+
+    The toolbar requires either the toolbars to be unspecified or
+    ``django.template.loaders.app_directories.Loader`` to be
+    included in the loaders.
+    If custom loaders are specified, then APP_DIRS must be True.
+    """
+    app_dirs = config.get("APP_DIRS", False)
+    loaders = config.get("OPTIONS", {}).get("loaders", None)
+    # By default the app loader is included.
+    has_app_loaders = (
+        loaders is None or "django.template.loaders.app_directories.Loader" in loaders
+    )
+    return has_app_loaders or app_dirs
+
+
 @register
 def check_middleware(app_configs, **kwargs):
     from debug_toolbar.middleware import DebugToolbarMiddleware
@@ -30,13 +48,16 @@ def check_middleware(app_configs, **kwargs):
     gzip_index = None
     debug_toolbar_indexes = []
 
-    if all(not config.get("APP_DIRS", False) for config in settings.TEMPLATES):
+    if all(not check_template_config(config) for config in settings.TEMPLATES):
         errors.append(
             Warning(
                 "At least one DjangoTemplates TEMPLATES configuration needs "
-                "to have APP_DIRS set to True.",
+                "to use django.template.loaders.app_directories.Loader or "
+                "have APP_DIRS set to True.",
                 hint=(
-                    "Use APP_DIRS=True for at least one "
+                    "Include django.template.loaders.app_directories.Loader "
+                    'in ["OPTIONS"]["loaders"]. Alternatively use '
+                    "APP_DIRS=True for at least one "
                     "django.template.backends.django.DjangoTemplates "
                     "backend configuration."
                 ),
diff --git a/docs/changes.rst b/docs/changes.rst
index a24be5ce7..76c839252 100644
--- a/docs/changes.rst
+++ b/docs/changes.rst
@@ -5,6 +5,8 @@ Next version
 ------------
 
 * Removed support for Django < 3.2.
+* Updated check ``W006`` to look for
+  ``django.template.loaders.app_directories.Loader``.
 
 3.2.4 (2021-12-15)
 ------------------
diff --git a/docs/checks.rst b/docs/checks.rst
index 4d4882db6..1140d6b49 100644
--- a/docs/checks.rst
+++ b/docs/checks.rst
@@ -15,4 +15,6 @@ Debug Toolbar setup and configuration:
   ``MIDDLEWARE_CLASSES`` setting.
 * **debug_toolbar.W005**: Setting ``DEBUG_TOOLBAR_PANELS`` is empty.
 * **debug_toolbar.W006**: At least one ``DjangoTemplates`` ``TEMPLATES``
-  configuration needs to have ``APP_DIRS`` set to ``True``.
+  configuration needs to have
+  ``django.template.loaders.app_directories.Loader`` included in
+  ``["OPTIONS"]["loaders"]`` or ``APP_DIRS`` set to ``True``.
diff --git a/tests/test_checks.py b/tests/test_checks.py
index 15464f9a2..1e24688da 100644
--- a/tests/test_checks.py
+++ b/tests/test_checks.py
@@ -134,21 +134,27 @@ def test_panels_is_empty(self):
                         "django.template.context_processors.request",
                         "django.contrib.auth.context_processors.auth",
                         "django.contrib.messages.context_processors.messages",
-                    ]
+                    ],
+                    "loaders": [
+                        "django.template.loaders.filesystem.Loader",
+                    ],
                 },
             },
         ]
     )
-    def test_templates_is_using_app_dirs_false(self):
+    def test_check_w006_invalid(self):
         errors = run_checks()
         self.assertEqual(
             errors,
             [
                 Warning(
-                    "At least one DjangoTemplates TEMPLATES configuration "
-                    "needs to have APP_DIRS set to True.",
+                    "At least one DjangoTemplates TEMPLATES configuration needs "
+                    "to use django.template.loaders.app_directories.Loader or "
+                    "have APP_DIRS set to True.",
                     hint=(
-                        "Use APP_DIRS=True for at least one "
+                        "Include django.template.loaders.app_directories.Loader "
+                        'in ["OPTIONS"]["loaders"]. Alternatively use '
+                        "APP_DIRS=True for at least one "
                         "django.template.backends.django.DjangoTemplates "
                         "backend configuration."
                     ),
@@ -156,3 +162,39 @@ def test_templates_is_using_app_dirs_false(self):
                 )
             ],
         )
+
+    @override_settings(
+        TEMPLATES=[
+            {
+                "NAME": "use_loaders",
+                "BACKEND": "django.template.backends.django.DjangoTemplates",
+                "APP_DIRS": False,
+                "OPTIONS": {
+                    "context_processors": [
+                        "django.template.context_processors.debug",
+                        "django.template.context_processors.request",
+                        "django.contrib.auth.context_processors.auth",
+                        "django.contrib.messages.context_processors.messages",
+                    ],
+                    "loaders": [
+                        "django.template.loaders.app_directories.Loader",
+                    ],
+                },
+            },
+            {
+                "NAME": "use_app_dirs",
+                "BACKEND": "django.template.backends.django.DjangoTemplates",
+                "APP_DIRS": True,
+                "OPTIONS": {
+                    "context_processors": [
+                        "django.template.context_processors.debug",
+                        "django.template.context_processors.request",
+                        "django.contrib.auth.context_processors.auth",
+                        "django.contrib.messages.context_processors.messages",
+                    ],
+                },
+            },
+        ]
+    )
+    def test_check_w006_valid(self):
+        self.assertEqual(run_checks(), [])