diff --git a/changelog.d/10768.misc b/changelog.d/10768.misc
new file mode 100644
index 0000000000000000000000000000000000000000..afd64ca1b00e72f40b2c6643c0017a54fd4b8525
--- /dev/null
+++ b/changelog.d/10768.misc
@@ -0,0 +1 @@
+Print a warning when using one of the deprecated `template_dir` settings.
diff --git a/synapse/config/account_validity.py b/synapse/config/account_validity.py
index 52e63ab1f6f2800012385db7016450f1503aa0fd..ffaffc4931a3fe3a37288e41281b75581189601b 100644
--- a/synapse/config/account_validity.py
+++ b/synapse/config/account_validity.py
@@ -11,8 +11,20 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
+import logging
+
 from synapse.config._base import Config, ConfigError
 
+logger = logging.getLogger(__name__)
+
+LEGACY_TEMPLATE_DIR_WARNING = """
+This server's configuration file is using the deprecated 'template_dir' setting in the
+'account_validity' section. Support for this setting has been deprecated and will be
+removed in a future version of Synapse. Server admins should instead use the new
+'custom_templates_directory' setting documented here:
+https://matrix-org.github.io/synapse/latest/templates.html
+---------------------------------------------------------------------------------------"""
+
 
 class AccountValidityConfig(Config):
     section = "account_validity"
@@ -69,6 +81,8 @@ class AccountValidityConfig(Config):
 
         # Load account validity templates.
         account_validity_template_dir = account_validity_config.get("template_dir")
+        if account_validity_template_dir is not None:
+            logger.warning(LEGACY_TEMPLATE_DIR_WARNING)
 
         account_renewed_template_filename = account_validity_config.get(
             "account_renewed_html_path", "account_renewed.html"
diff --git a/synapse/config/emailconfig.py b/synapse/config/emailconfig.py
index 4477419196c20f5fbc78f2a160003155f7d05159..936abe6178cb80a5df0eb4c9eb9f20f199bc9a9c 100644
--- a/synapse/config/emailconfig.py
+++ b/synapse/config/emailconfig.py
@@ -16,6 +16,7 @@
 
 # This file can't be called email.py because if it is, we cannot:
 import email.utils
+import logging
 import os
 from enum import Enum
 from typing import Optional
@@ -24,6 +25,8 @@ import attr
 
 from ._base import Config, ConfigError
 
+logger = logging.getLogger(__name__)
+
 MISSING_PASSWORD_RESET_CONFIG_ERROR = """\
 Password reset emails are enabled on this homeserver due to a partial
 'email' block. However, the following required keys are missing:
@@ -44,6 +47,14 @@ DEFAULT_SUBJECTS = {
     "email_validation": "[%(server_name)s] Validate your email",
 }
 
+LEGACY_TEMPLATE_DIR_WARNING = """
+This server's configuration file is using the deprecated 'template_dir' setting in the
+'email' section. Support for this setting has been deprecated and will be removed in a
+future version of Synapse. Server admins should instead use the new
+'custom_templates_directory' setting documented here:
+https://matrix-org.github.io/synapse/latest/templates.html
+---------------------------------------------------------------------------------------"""
+
 
 @attr.s(slots=True, frozen=True)
 class EmailSubjectConfig:
@@ -105,6 +116,9 @@ class EmailConfig(Config):
 
         # A user-configurable template directory
         template_dir = email_config.get("template_dir")
+        if template_dir is not None:
+            logger.warning(LEGACY_TEMPLATE_DIR_WARNING)
+
         if isinstance(template_dir, str):
             # We need an absolute path, because we change directory after starting (and
             # we don't yet know what auxiliary templates like mail.css we will need).
diff --git a/synapse/config/sso.py b/synapse/config/sso.py
index fe1177ab810975f0c346d5ee220c93c9554614c5..524a7ff3aaf336b7308d0593cc2de8d942058bad 100644
--- a/synapse/config/sso.py
+++ b/synapse/config/sso.py
@@ -11,12 +11,23 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
+import logging
 from typing import Any, Dict, Optional
 
 import attr
 
 from ._base import Config
 
+logger = logging.getLogger(__name__)
+
+LEGACY_TEMPLATE_DIR_WARNING = """
+This server's configuration file is using the deprecated 'template_dir' setting in the
+'sso' section. Support for this setting has been deprecated and will be removed in a
+future version of Synapse. Server admins should instead use the new
+'custom_templates_directory' setting documented here:
+https://matrix-org.github.io/synapse/latest/templates.html
+---------------------------------------------------------------------------------------"""
+
 
 @attr.s(frozen=True)
 class SsoAttributeRequirement:
@@ -43,6 +54,8 @@ class SSOConfig(Config):
 
         # The sso-specific template_dir
         self.sso_template_dir = sso_config.get("template_dir")
+        if self.sso_template_dir is not None:
+            logger.warning(LEGACY_TEMPLATE_DIR_WARNING)
 
         # Read templates from disk
         custom_template_directories = (