diff --git a/jenkins_jobs/modules/project_githuborg.py b/jenkins_jobs/modules/project_githuborg.py
index 45577e990..75a8fa6b7 100644
--- a/jenkins_jobs/modules/project_githuborg.py
+++ b/jenkins_jobs/modules/project_githuborg.py
@@ -246,8 +246,14 @@ def github_org(xml_parent, data):
     :extensions:
 
         * **clean** (`dict`)
-            * **after** (`bool`) - Clean the workspace after checkout
-            * **before** (`bool`) - Clean the workspace before checkout
+            * **after** (`dict`) - Clean the workspace after checkout
+                * **remove-stale-nested-repos** (`bool`) - Deletes untracked
+                  submodules and any other subdirectories which contain .git directories
+                  (default false)
+            * **before** (`dict`) - Clean the workspace before checkout
+                * **remove-stale-nested-repos** (`bool`) - Deletes untracked
+                  submodules and any other subdirectories which contain .git directories
+                  (default false)
         * **depth** (`int`) - Set shallow clone depth (default 1)
         * **disable-pr-notifications** (`bool`) - Disable default github status
             notifications on pull requests (default false) (Requires the
diff --git a/jenkins_jobs/modules/project_multibranch.py b/jenkins_jobs/modules/project_multibranch.py
index ac85974fb..44d87a3bb 100644
--- a/jenkins_jobs/modules/project_multibranch.py
+++ b/jenkins_jobs/modules/project_multibranch.py
@@ -427,8 +427,14 @@ def bitbucket_scm(xml_parent, data):
     :extensions:
 
         * **clean** (`dict`)
-            * **after** (`bool`) - Clean the workspace after checkout
-            * **before** (`bool`) - Clean the workspace before checkout
+            * **after** (`dict`) - Clean the workspace after checkout
+                * **remove-stale-nested-repos** (`bool`) - Deletes untracked
+                  submodules and any other subdirectories which contain .git directories
+                  (default false)
+            * **before** (`dict`) - Clean the workspace before checkout
+                * **remove-stale-nested-repos** (`bool`) - Deletes untracked
+                  submodules and any other subdirectories which contain .git directories
+                  (default false)
         * **prune** (`bool`) - Prune remote branches (default false)
         * **shallow-clone** (`bool`) - Perform shallow clone (default false)
         * **sparse-checkout** (dict)
@@ -678,8 +684,14 @@ def gerrit_scm(xml_parent, data):
     :extensions:
 
         * **clean** (`dict`)
-            * **after** (`bool`) - Clean the workspace after checkout
-            * **before** (`bool`) - Clean the workspace before checkout
+            * **after** (`dict`) - Clean the workspace after checkout
+                * **remove-stale-nested-repos** (`bool`) - Deletes untracked
+                  submodules and any other subdirectories which contain .git directories
+                  (default false)
+            * **before** (`dict`) - Clean the workspace before checkout
+                * **remove-stale-nested-repos** (`bool`) - Deletes untracked
+                  submodules and any other subdirectories which contain .git directories
+                  (default false)
         * **prune** (`bool`) - Prune remote branches (default false)
         * **shallow-clone** (`bool`) - Perform shallow clone (default false)
         * **sparse-checkout** (dict)
@@ -848,8 +860,14 @@ def git_scm(xml_parent, data):
     :extensions:
 
         * **clean** (`dict`)
-            * **after** (`bool`) - Clean the workspace after checkout
-            * **before** (`bool`) - Clean the workspace before checkout
+            * **after** (`dict`) - Clean the workspace after checkout
+                * **remove-stale-nested-repos** (`bool`) - Deletes untracked
+                  submodules and any other subdirectories which contain .git directories
+                  (default false)
+            * **before** (`dict`) - Clean the workspace before checkout
+                * **remove-stale-nested-repos** (`bool`) - Deletes untracked
+                  submodules and any other subdirectories which contain .git directories
+                  (default false)
         * **prune** (`bool`) - Prune remote branches (default false)
         * **shallow-clone** (`bool`) - Perform shallow clone (default false)
         * **sparse-checkout** (dict)
@@ -1006,8 +1024,14 @@ def github_scm(xml_parent, data):
     :extensions:
 
         * **clean** (`dict`)
-            * **after** (`bool`) - Clean the workspace after checkout
-            * **before** (`bool`) - Clean the workspace before checkout
+            * **after** (`dict`) - Clean the workspace after checkout
+                * **remove-stale-nested-repos** (`bool`) - Deletes untracked
+                    submodules and any other subdirectories which contain .git directories
+                    (default false)
+            * **before** (`dict`) - Clean the workspace before checkout
+                * **remove-stale-nested-repos** (`bool`) - Deletes untracked
+                    submodules and any other subdirectories which contain .git directories
+                    (default false)
         * **prune** (`bool`) - Prune remote branches (default false)
         * **shallow-clone** (`bool`) - Perform shallow clone (default false)
         * **sparse-checkout** (dict)
diff --git a/jenkins_jobs/modules/scm.py b/jenkins_jobs/modules/scm.py
index d5681e718..53716a481 100644
--- a/jenkins_jobs/modules/scm.py
+++ b/jenkins_jobs/modules/scm.py
@@ -262,8 +262,14 @@ def git(registry, xml_parent, data):
             to build. Can be one of `default`,`inverse`, or `gerrit`
             (default 'default')
         * **clean** (`dict`)
-            * **after** (`bool`) - Clean the workspace after checkout
-            * **before** (`bool`) - Clean the workspace before checkout
+            * **after** (`dict`) - Clean the workspace after checkout
+                * **remove-stale-nested-repos** (`bool`) - Deletes untracked
+                  submodules and any other subdirectories which contain .git directories
+                  (default false)
+            * **before** (`dict`) - Clean the workspace before checkout
+                * **remove-stale-nested-repos** (`bool`) - Deletes untracked
+                  submodules and any other subdirectories which contain .git directories
+                  (default false)
         * **committer** (`dict`)
             * **name** (`str`) - Name to use as author of new commits
             * **email** (`str`) - E-mail address to use for new commits
@@ -518,7 +524,17 @@ def git_extensions(xml_parent, data):
         else:
             clean_after = data["clean"].get("after", False)
             clean_before = data["clean"].get("before", False)
-        if clean_after:
+        if clean_after is not False:
+            if isinstance(clean_after, bool):
+                clean_after_opts = {}
+                logger.warning(
+                    "'clean: after: bool' configuration format is deprecated, "
+                    "after should be an empty dict or filled with accepted "
+                    "options."
+                )
+            else:
+                clean_after_opts = clean_after
+
             ext_name = impl_prefix + "CleanCheckout"
             if trait:
                 trait_name = "CleanAfterCheckoutTrait"
@@ -526,7 +542,20 @@ def git_extensions(xml_parent, data):
                 ext = XML.SubElement(tr, "extension", {"class": ext_name})
             else:
                 ext = XML.SubElement(xml_parent, ext_name)
-        if clean_before:
+            if "remove-stale-nested-repos" in clean_after_opts:
+                elm = XML.SubElement(ext, "deleteUntrackedNestedRepositories")
+                elm.text = "true"
+        if clean_before is not False:
+            if isinstance(clean_before, bool):
+                clean_before_opts = {}
+                logger.warning(
+                    "'clean: before: bool' configuration format is deprecated, "
+                    "before should be an empty dict or filled with accepted "
+                    "options."
+                )
+            else:
+                clean_before_opts = clean_before
+
             ext_name = impl_prefix + "CleanBeforeCheckout"
             if trait:
                 trait_name = "CleanBeforeCheckoutTrait"
@@ -534,6 +563,9 @@ def git_extensions(xml_parent, data):
                 ext = XML.SubElement(tr, "extension", {"class": ext_name})
             else:
                 ext = XML.SubElement(xml_parent, ext_name)
+            if "remove-stale-nested-repos" in clean_before_opts:
+                elm = XML.SubElement(ext, "deleteUntrackedNestedRepositories")
+                elm.text = "true"
     committer = data.get("committer", {})
     if committer:
         ext_name = impl_prefix + "UserIdentity"
diff --git a/tests/scm/fixtures/git-clean02.xml b/tests/scm/fixtures/git-clean02.xml
new file mode 100644
index 000000000..11c9223d9
--- /dev/null
+++ b/tests/scm/fixtures/git-clean02.xml
@@ -0,0 +1,36 @@
+<?xml version="1.0" encoding="utf-8"?>
+<project>
+  <scm class="hudson.plugins.git.GitSCM">
+    <configVersion>2</configVersion>
+    <userRemoteConfigs>
+      <hudson.plugins.git.UserRemoteConfig>
+        <name>origin</name>
+        <refspec>+refs/heads/*:refs/remotes/origin/*</refspec>
+        <url>https://github.com/openstack-infra/jenkins-job-builder.git</url>
+      </hudson.plugins.git.UserRemoteConfig>
+    </userRemoteConfigs>
+    <branches>
+      <hudson.plugins.git.BranchSpec>
+        <name>**</name>
+      </hudson.plugins.git.BranchSpec>
+    </branches>
+    <disableSubmodules>false</disableSubmodules>
+    <recursiveSubmodules>false</recursiveSubmodules>
+    <doGenerateSubmoduleConfigurations>false</doGenerateSubmoduleConfigurations>
+    <remotePoll>false</remotePoll>
+    <gitTool>Default</gitTool>
+    <submoduleCfg class="list"/>
+    <reference/>
+    <gitConfigName/>
+    <gitConfigEmail/>
+    <extensions>
+      <hudson.plugins.git.extensions.impl.CleanCheckout>
+        <deleteUntrackedNestedRepositories>true</deleteUntrackedNestedRepositories>
+      </hudson.plugins.git.extensions.impl.CleanCheckout>
+      <hudson.plugins.git.extensions.impl.CleanBeforeCheckout>
+        <deleteUntrackedNestedRepositories>true</deleteUntrackedNestedRepositories>
+      </hudson.plugins.git.extensions.impl.CleanBeforeCheckout>
+      <hudson.plugins.git.extensions.impl.WipeWorkspace/>
+    </extensions>
+  </scm>
+</project>
diff --git a/tests/scm/fixtures/git-clean02.yaml b/tests/scm/fixtures/git-clean02.yaml
new file mode 100644
index 000000000..8e2ae767b
--- /dev/null
+++ b/tests/scm/fixtures/git-clean02.yaml
@@ -0,0 +1,8 @@
+scm:
+    - git:
+        url: https://github.com/openstack-infra/jenkins-job-builder.git
+        clean:
+            after:
+                remove-stale-nested-repos: true
+            before:
+                remove-stale-nested-repos: true
diff --git a/tests/scm/fixtures/git-clean03.xml b/tests/scm/fixtures/git-clean03.xml
new file mode 100644
index 000000000..f742cf4fb
--- /dev/null
+++ b/tests/scm/fixtures/git-clean03.xml
@@ -0,0 +1,32 @@
+<?xml version="1.0" encoding="utf-8"?>
+<project>
+  <scm class="hudson.plugins.git.GitSCM">
+    <configVersion>2</configVersion>
+    <userRemoteConfigs>
+      <hudson.plugins.git.UserRemoteConfig>
+        <name>origin</name>
+        <refspec>+refs/heads/*:refs/remotes/origin/*</refspec>
+        <url>https://github.com/openstack-infra/jenkins-job-builder.git</url>
+      </hudson.plugins.git.UserRemoteConfig>
+    </userRemoteConfigs>
+    <branches>
+      <hudson.plugins.git.BranchSpec>
+        <name>**</name>
+      </hudson.plugins.git.BranchSpec>
+    </branches>
+    <disableSubmodules>false</disableSubmodules>
+    <recursiveSubmodules>false</recursiveSubmodules>
+    <doGenerateSubmoduleConfigurations>false</doGenerateSubmoduleConfigurations>
+    <remotePoll>false</remotePoll>
+    <gitTool>Default</gitTool>
+    <submoduleCfg class="list"/>
+    <reference/>
+    <gitConfigName/>
+    <gitConfigEmail/>
+    <extensions>
+      <hudson.plugins.git.extensions.impl.CleanCheckout/>
+      <hudson.plugins.git.extensions.impl.CleanBeforeCheckout/>
+      <hudson.plugins.git.extensions.impl.WipeWorkspace/>
+    </extensions>
+  </scm>
+</project>
diff --git a/tests/scm/fixtures/git-clean03.yaml b/tests/scm/fixtures/git-clean03.yaml
new file mode 100644
index 000000000..49a3e25f1
--- /dev/null
+++ b/tests/scm/fixtures/git-clean03.yaml
@@ -0,0 +1,6 @@
+scm:
+    - git:
+        url: https://github.com/openstack-infra/jenkins-job-builder.git
+        clean:
+            after: {}
+            before: {}