diff --git a/changelog.d/13077.doc b/changelog.d/13077.doc
new file mode 100644
index 0000000000000000000000000000000000000000..502f2d059e9f19ce715de0cbdeeca3a0ba13aafc
--- /dev/null
+++ b/changelog.d/13077.doc
@@ -0,0 +1,3 @@
+Clean up references to sample configuration and redirect users to the configuration manual instead.
+
+
diff --git a/docs/admin_api/user_admin_api.md b/docs/admin_api/user_admin_api.md
index 62f89e8cba67f13f187da2395fb41c2807741ac9..1235f1cb950eaeb60704a7698d83f8ddcc2a422d 100644
--- a/docs/admin_api/user_admin_api.md
+++ b/docs/admin_api/user_admin_api.md
@@ -124,9 +124,8 @@ Body parameters:
   - `address` - string. Value of third-party ID.
   belonging to a user.
 - `external_ids` - array, optional. Allow setting the identifier of the external identity
-  provider for SSO (Single sign-on). Details in
-  [Sample Configuration File](../usage/configuration/homeserver_sample_config.html)
-  section `sso` and `oidc_providers`.
+  provider for SSO (Single sign-on). Details in the configuration manual under the
+  sections [sso](../usage/configuration/config_documentation.md#sso) and [oidc_providers](../usage/configuration/config_documentation.md#oidc_providers).
   - `auth_provider` - string. ID of the external identity provider. Value of `idp_id`
     in the homeserver configuration. Note that no error is raised if the provided
     value is not in the homeserver configuration.
diff --git a/docs/code_style.md b/docs/code_style.md
index db7edcd76b6953ab9d763166ac56baf339ec06e5..d65fda62d140cd064896c1a8d715138d2e0c886a 100644
--- a/docs/code_style.md
+++ b/docs/code_style.md
@@ -70,82 +70,61 @@ on save as they take a while and can be very resource intensive.
     -   Avoid wildcard imports (`from synapse.types import *`) and
         relative imports (`from .types import UserID`).
 
-## Configuration file format
+## Configuration code and documentation format
 
-The [sample configuration file](./sample_config.yaml) acts as a
+When adding a configuration option to the code, if several settings are grouped into a single dict, ensure that your code
+correctly handles the top-level option being set to `None` (as it will be if no sub-options are enabled).
+
+The [configuration manual](usage/configuration/config_documentation.md) acts as a
 reference to Synapse's configuration options for server administrators.
 Remember that many readers will be unfamiliar with YAML and server
-administration in general, so that it is important that the file be as
-easy to understand as possible, which includes following a consistent
-format.
+administration in general, so it is important that when you add
+a configuration option the documentation be as easy to understand as possible, which 
+includes following a consistent format.
 
 Some guidelines follow:
 
--   Sections should be separated with a heading consisting of a single
-    line prefixed and suffixed with `##`. There should be **two** blank
-    lines before the section header, and **one** after.
--   Each option should be listed in the file with the following format:
-    -   A comment describing the setting. Each line of this comment
-        should be prefixed with a hash (`#`) and a space.
+- Each option should be listed in the config manual with the following format:
+      
+    - The name of the option, prefixed by `###`. 
 
-        The comment should describe the default behaviour (ie, what
+    - A comment which describes the default behaviour (i.e. what
         happens if the setting is omitted), as well as what the effect
         will be if the setting is changed.
-
-        Often, the comment end with something like "uncomment the
-        following to <do action>".
-
-    -   A line consisting of only `#`.
-    -   A commented-out example setting, prefixed with only `#`.
+    - An example setting, using backticks to define the code block
 
         For boolean (on/off) options, convention is that this example
-        should be the *opposite* to the default (so the comment will end
-        with "Uncomment the following to enable [or disable]
-        <feature>." For other options, the example should give some
-        non-default value which is likely to be useful to the reader.
-
--   There should be a blank line between each option.
--   Where several settings are grouped into a single dict, *avoid* the
-    convention where the whole block is commented out, resulting in
-    comment lines starting `# #`, as this is hard to read and confusing
-    to edit. Instead, leave the top-level config option uncommented, and
-    follow the conventions above for sub-options. Ensure that your code
-    correctly handles the top-level option being set to `None` (as it
-    will be if no sub-options are enabled).
--   Lines should be wrapped at 80 characters.
--   Use two-space indents.
--   `true` and `false` are spelt thus (as opposed to `True`, etc.)
--   Use single quotes (`'`) rather than double-quotes (`"`) or backticks
-    (`` ` ``) to refer to configuration options.
+        should be the *opposite* to the default. For other options, the example should give
+        some non-default value which is likely to be useful to the reader.
+
+- There should be a horizontal rule between each option, which can be achieved by adding `---` before and
+  after the option.
+- `true` and `false` are spelt thus (as opposed to `True`, etc.)
 
 Example:
 
+---
+### `modules`
+
+Use the `module` sub-option to add a module under `modules` to extend functionality. 
+The `module` setting then has a sub-option, `config`, which can be used to define some configuration
+for the `module`.
+
+Defaults to none.
+
+Example configuration:
 ```yaml
-## Frobnication ##
-
-# The frobnicator will ensure that all requests are fully frobnicated.
-# To enable it, uncomment the following.
-#
-#frobnicator_enabled: true
-
-# By default, the frobnicator will frobnicate with the default frobber.
-# The following will make it use an alternative frobber.
-#
-#frobincator_frobber: special_frobber
-
-# Settings for the frobber
-#
-frobber:
-  # frobbing speed. Defaults to 1.
-  #
-  #speed: 10
-
-  # frobbing distance. Defaults to 1000.
-  #
-  #distance: 100
+modules:
+  - module: my_super_module.MySuperClass
+    config:
+      do_thing: true
+  - module: my_other_super_module.SomeClass
+    config: {}
 ```
+---
 
 Note that the sample configuration is generated from the synapse code
 and is maintained by a script, `scripts-dev/generate_sample_config.sh`.
 Making sure that the output from this script matches the desired format
 is left as an exercise for the reader!
+
diff --git a/docs/jwt.md b/docs/jwt.md
index 8f859d59a6d9e94e5ab1d579c05587599ffa4e45..2e262583a7cedc6ec78341ae6da6e27f209cddd5 100644
--- a/docs/jwt.md
+++ b/docs/jwt.md
@@ -49,9 +49,8 @@ as follows:
 * For other installation mechanisms, see the documentation provided by the
   maintainer.
 
-To enable the JSON web token integration, you should then add a `jwt_config` section
-to your configuration file (or uncomment the `enabled: true` line in the
-existing section). See [sample_config.yaml](./sample_config.yaml) for some
+To enable the JSON web token integration, you should then add a `jwt_config` option
+to your configuration file. See the [configuration manual](usage/configuration/config_documentation.md#jwt_config) for some
 sample settings.
 
 ## How to test JWT as a developer
diff --git a/docs/manhole.md b/docs/manhole.md
index a82fad0f0fe05e8b5213511fde8b1831ffb732c0..4e5bf833ce555abb4d5e1f746fa6d0100bafc150 100644
--- a/docs/manhole.md
+++ b/docs/manhole.md
@@ -13,8 +13,10 @@ environments where untrusted users have shell access.
 
 ## Configuring the manhole
 
-To enable it, first uncomment the `manhole` listener configuration in
-`homeserver.yaml`. The configuration is slightly different if you're using docker.
+To enable it, first add the `manhole` listener configuration in your
+`homeserver.yaml`. You can find information on how to do that 
+in the [configuration manual](usage/configuration/config_documentation.md#manhole_settings).
+The configuration is slightly different if you're using docker.
 
 #### Docker config
 
diff --git a/docs/message_retention_policies.md b/docs/message_retention_policies.md
index b52c4aaa2425a785707cd2f47790d1a941c63722..8c88f939356dde7a628f3937dd2a816f377d0bd5 100644
--- a/docs/message_retention_policies.md
+++ b/docs/message_retention_policies.md
@@ -49,9 +49,9 @@ clients.
 
 ## Server configuration
 
-Support for this feature can be enabled and configured in the
-`retention` section of the Synapse configuration file (see the
-[sample file](https://github.com/matrix-org/synapse/blob/v1.36.0/docs/sample_config.yaml#L451-L518)).
+Support for this feature can be enabled and configured by adding a the
+`retention` in the Synapse configuration file (see
+[configuration manual](usage/configuration/config_documentation.md#retention)).
 
 To enable support for message retention policies, set the setting
 `enabled` in this section to `true`.
@@ -65,8 +65,8 @@ message retention policy configured in its state. This allows server
 admins to ensure that messages are never kept indefinitely in a server's
 database. 
 
-A default policy can be defined as such, in the `retention` section of
-the configuration file:
+A default policy can be defined as such, by adding the `retention` option in
+the configuration file and adding these sub-options:
 
 ```yaml
 default_policy:
@@ -86,8 +86,8 @@ Purge jobs are the jobs that Synapse runs in the background to purge
 expired events from the database. They are only run if support for
 message retention policies is enabled in the server's configuration. If
 no configuration for purge jobs is configured by the server admin,
-Synapse will use a default configuration, which is described in the
-[sample configuration file](https://github.com/matrix-org/synapse/blob/v1.36.0/docs/sample_config.yaml#L451-L518).
+Synapse will use a default configuration, which is described here in the
+[configuration manual](usage/configuration/config_documentation.md#retention).
 
 Some server admins might want a finer control on when events are removed
 depending on an event's room's policy. This can be done by setting the
@@ -137,8 +137,8 @@ the server's database.
 ### Lifetime limits
 
 Server admins can set limits on the values of `max_lifetime` to use when
-purging old events in a room. These limits can be defined as such in the
-`retention` section of the configuration file:
+purging old events in a room. These limits can be defined under the
+`retention` option in the configuration file:
 
 ```yaml
 allowed_lifetime_min: 1d
diff --git a/docs/openid.md b/docs/openid.md
index 9d615a573759035ed3707226177e1431a28635dc..d0ccf36f71f77c0e9cb59679119e70e504b1be30 100644
--- a/docs/openid.md
+++ b/docs/openid.md
@@ -45,8 +45,8 @@ as follows:
    maintainer.
 
 To enable the OpenID integration, you should then add a section to the `oidc_providers`
-setting in your configuration file (or uncomment one of the existing examples).
-See [sample_config.yaml](./sample_config.yaml) for some sample settings, as well as
+setting in your configuration file.
+See the [configuration manual](usage/configuration/config_documentation.md#oidc_providers) for some sample settings, as well as
 the text below for example configurations for specific providers.
 
 ## Sample configs
diff --git a/docs/setup/forward_proxy.md b/docs/setup/forward_proxy.md
index 494c14893b26a99ed00d8adb08f50d1f8976f7e7..3482691f8328b1a981bdda7c50acdfddfc8961d7 100644
--- a/docs/setup/forward_proxy.md
+++ b/docs/setup/forward_proxy.md
@@ -66,8 +66,8 @@ in Synapse can be deactivated.
 
 **NOTE**: This has an impact on security and is for testing purposes only!
 
-To deactivate the certificate validation, the following setting must be made in
-[homserver.yaml](../usage/configuration/homeserver_sample_config.md).
+To deactivate the certificate validation, the following setting must be added to
+your [homserver.yaml](../usage/configuration/homeserver_sample_config.md).
 
 ```yaml
 use_insecure_ssl_client_just_for_testing_do_not_use: true
diff --git a/docs/setup/installation.md b/docs/setup/installation.md
index 1580529fd1c2adb49647174f87e6f7c404691300..260e50577b5da36e6b1c2a53e5e55b8a79148cce 100644
--- a/docs/setup/installation.md
+++ b/docs/setup/installation.md
@@ -407,11 +407,11 @@ The recommended way to do so is to set up a reverse proxy on port
 Alternatively, you can configure Synapse to expose an HTTPS port. To do
 so, you will need to edit `homeserver.yaml`, as follows:
 
-- First, under the `listeners` section, uncomment the configuration for the
-  TLS-enabled listener. (Remove the hash sign (`#`) at the start of
-  each line). The relevant lines are like this:
+- First, under the `listeners` option, add the configuration for the
+  TLS-enabled listener like so:
 
 ```yaml
+listeners:
   - port: 8448
     type: http
     tls: true
@@ -419,9 +419,11 @@ so, you will need to edit `homeserver.yaml`, as follows:
       - names: [client, federation]
   ```
 
-- You will also need to uncomment the `tls_certificate_path` and
-  `tls_private_key_path` lines under the `TLS` section. You will need to manage
-  provisioning of these certificates yourself.
+- You will also need to add the options `tls_certificate_path` and
+  `tls_private_key_path`. to your configuration file. You will need to manage provisioning of 
+   these certificates yourself.
+- You can find more information about these options as well as how to configure synapse in the 
+  [configuration manual](../usage/configuration/config_documentation.md).
 
   If you are using your own certificate, be sure to use a `.pem` file that
   includes the full certificate chain including any intermediate certificates
diff --git a/docs/usage/configuration/config_documentation.md b/docs/usage/configuration/config_documentation.md
index 19eb504496b262e7342dd6b38717428a571e3cd2..82edd53e368567a08a7431a03ac850756ac3427c 100644
--- a/docs/usage/configuration/config_documentation.md
+++ b/docs/usage/configuration/config_documentation.md
@@ -2999,7 +2999,7 @@ This setting has the following sub-options:
 * `localdb_enabled`: Set to false to disable authentication against the local password
    database. This is ignored if `enabled` is false, and is only useful
    if you have other `password_providers`. Defaults to true. 
-* `pepper`: Set the value here to a secret random string for extra security. # Uncomment and change to a secret random string for extra security.
+* `pepper`: Set the value here to a secret random string for extra security.
    DO NOT CHANGE THIS AFTER INITIAL SETUP!
 * `policy`: Define and enforce a password policy, such as minimum lengths for passwords, etc. 
    Each parameter is optional. This is an implementation of MSC2000. Parameters are as follows:
diff --git a/docs/usage/configuration/user_authentication/single_sign_on/cas.md b/docs/usage/configuration/user_authentication/single_sign_on/cas.md
index 3bac1b29f0511cf44b9c50a492af9b8f37370fd9..899face876426ac87c93d2388e71c75b696a5cf5 100644
--- a/docs/usage/configuration/user_authentication/single_sign_on/cas.md
+++ b/docs/usage/configuration/user_authentication/single_sign_on/cas.md
@@ -4,5 +4,5 @@ Synapse supports authenticating users via the [Central Authentication
 Service protocol](https://en.wikipedia.org/wiki/Central_Authentication_Service)
 (CAS) natively.
 
-Please see the `cas_config` and `sso` sections of the [Synapse configuration
-file](../../../configuration/homeserver_sample_config.md) for more details.
\ No newline at end of file
+Please see the [cas_config](../../../configuration/config_documentation.md#cas_config) and [sso](../../../configuration/config_documentation.md#sso)
+sections of the configuration manual for more details.
\ No newline at end of file
diff --git a/synapse/config/emailconfig.py b/synapse/config/emailconfig.py
index c82f3ee7a3c4d210d233aaeb062ecf3ab005d33a..6e11fbdb9ac907c9ff86c97d7fc6a2a553ebabb5 100644
--- a/synapse/config/emailconfig.py
+++ b/synapse/config/emailconfig.py
@@ -145,7 +145,7 @@ class EmailConfig(Config):
             raise ConfigError(
                 'The config option "trust_identity_server_for_password_resets" '
                 'has been replaced by "account_threepid_delegate". '
-                "Please consult the sample config at docs/sample_config.yaml for "
+                "Please consult the configuration manual at docs/usage/configuration/config_documentation.md for "
                 "details and update your config file."
             )