diff --git a/data/deprecations/16-10-omnibus-gitconfig-deprecation.yml b/data/deprecations/16-10-omnibus-gitconfig-deprecation.yml
new file mode 100644
index 0000000000000000000000000000000000000000..e46a8f7a900e4c27733502e8d3094f792c0513e1
--- /dev/null
+++ b/data/deprecations/16-10-omnibus-gitconfig-deprecation.yml
@@ -0,0 +1,51 @@
+- title: "`Gitlab['omnibus_gitconfig']` configuration item is deprecated"
+  # The milestones for the deprecation announcement, and the removal.
+  removal_milestone: "17.0"
+  announcement_milestone: "16.10"
+  # Change breaking_change to false if needed.
+  breaking_change: true
+  # The stage and GitLab username of the person reporting the change,
+  # and a link to the deprecation issue
+  reporter: samihiltunen
+  stage: systems
+  issue_url: https://gitlab.com/gitlab-org/gitaly/-/issues/5132
+  impact: low # Can be one of: [critical, high, medium, low]
+  scope: instance # Can be one or a combination of: [instance, group, project]
+  resolution_role: Admin  # Can be one of: [Admin, Owner, Maintainer, Developer]
+  manual_task: true # Can be true or false. Use this to denote whether a resolution action must be performed manually (true), or if it can be automated by using the API or other automation (false).
+  body: |
+    The `omnibus_gitconfig['system']` configuration item has been deprecated. If you use
+    `omnibus_gitconfig['system']` to set custom Git configuration for Gitaly, you must configure Git
+    directly through Gitaly configuration under `gitaly[:configuration][:git][:config]` before upgrading to GitLab 17.0.
+
+    For example:
+
+    ```ruby
+      gitaly[:configuration][:git][:config] = [
+        {
+          key: 'fetch.fsckObjects',
+          value: 'true',
+        },
+        # ...
+      ]
+    ```
+
+    The format of the configuration keys must match what is passed to `git` through the CLI flag `git -c <configuration>`.
+
+    If you have trouble converting the existing keys to the expected format, see the existing keys in the correct format in
+    the Linux package-generated configuration file of Gitaly. By default, the configuration file is located at
+    `/var/opt/gitlab/gitaly/config.toml`.
+
+    The following configuration options that are managed by Gitaly should be removed. These keys do not need to be migrated
+    to Gitaly:
+
+    - `pack.threads=1`
+    - `receive.advertisePushOptions=true`
+    - `receive.fsckObjects=true`
+    - `repack.writeBitmaps=true`
+    - `transfer.hideRefs=^refs/tmp/`
+    - `transfer.hideRefs=^refs/keep-around/`
+    - `transfer.hideRefs=^refs/remotes/`
+    - `core.alternateRefsCommand="exit 0 #"`
+    - `core.fsyncObjectFiles=true`
+    - `fetch.writeCommitGraph=true`
diff --git a/doc/update/deprecations.md b/doc/update/deprecations.md
index 3d66106b68711577485ac79482ac09abc4c6d2dd..b32495d37f1904399e46d9822cd90d4328acb046 100644
--- a/doc/update/deprecations.md
+++ b/doc/update/deprecations.md
@@ -2052,6 +2052,54 @@ removed in 17.0.
 
 <div class="deprecation breaking-change" data-milestone="17.0">
 
+### `Gitlab['omnibus_gitconfig']` configuration item is deprecated
+
+<div class="deprecation-notes">
+- Announced in GitLab <span class="milestone">16.10</span>
+- Removal in GitLab <span class="milestone">17.0</span> ([breaking change](https://docs.gitlab.com/ee/update/terminology.html#breaking-change))
+- To discuss this change or learn more, see the [deprecation issue](https://gitlab.com/gitlab-org/gitaly/-/issues/5132).
+</div>
+
+The `omnibus_gitconfig['system']` configuration item has been deprecated. If you use
+`omnibus_gitconfig['system']` to set custom Git configuration for Gitaly, you must configure Git
+directly through Gitaly configuration under `gitaly[:configuration][:git][:config]` before upgrading to GitLab 17.0.
+
+For example:
+
+```ruby
+  gitaly[:configuration][:git][:config] = [
+    {
+      key: 'fetch.fsckObjects',
+      value: 'true',
+    },
+    # ...
+  ]
+```
+
+The format of the configuration keys must match what is passed to `git` through the CLI flag `git -c <configuration>`.
+
+If you have trouble converting the existing keys to the expected format, see the existing keys in the correct format in
+the Linux package-generated configuration file of Gitaly. By default, the configuration file is located at
+`/var/opt/gitlab/gitaly/config.toml`.
+
+The following configuration options that are managed by Gitaly should be removed. These keys do not need to be migrated
+to Gitaly:
+
+- `pack.threads=1`
+- `receive.advertisePushOptions=true`
+- `receive.fsckObjects=true`
+- `repack.writeBitmaps=true`
+- `transfer.hideRefs=^refs/tmp/`
+- `transfer.hideRefs=^refs/keep-around/`
+- `transfer.hideRefs=^refs/remotes/`
+- `core.alternateRefsCommand="exit 0 #"`
+- `core.fsyncObjectFiles=true`
+- `fetch.writeCommitGraph=true`
+
+</div>
+
+<div class="deprecation breaking-change" data-milestone="17.0">
+
 ### `after_script` keyword will run for cancelled jobs
 
 <div class="deprecation-notes">