diff --git a/man/repo-gc.1 b/man/repo-gc.1
index 5a8ac47..61b3949 100644
--- a/man/repo-gc.1
+++ b/man/repo-gc.1
@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man.
-.TH REPO "1" "June 2026" "repo gc" "Repo Manual"
+.TH REPO "1" "September 2026" "repo gc" "Repo Manual"
 .SH NAME
 repo \- repo gc - manual page for repo gc
 .SH SYNOPSIS
@@ -22,6 +22,9 @@
 .TP
 \fB\-\-repack\fR
 repack all projects that use partial clone with filter=blob:none
+.TP
+\fB\-\-keep\-manifest\-projects\fR
+keep Git data for projects still in the manifests
 .SS Logging options:
 .TP
 \fB\-v\fR, \fB\-\-verbose\fR
@@ -44,3 +47,11 @@
 operate on this manifest and its submanifests
 .PP
 Run `repo help gc` to view the detailed manual.
+.SH DETAILS
+.PP
+The 'repo gc' command removes internal Git data for projects that are no longer
+active in the current configuration.
+.PP
+Projects excluded by the configured manifest groups are inactive by default. Use
+\fB\-\-keep\-manifest\-projects\fR to keep Git data for projects that are still in the
+manifests.
diff --git a/subcmds/gc.py b/subcmds/gc.py
index 1d1023a..8b54f87 100644
--- a/subcmds/gc.py
+++ b/subcmds/gc.py
@@ -29,6 +29,14 @@
     helpUsage = """
 %prog
 """
+    helpDescription = """
+The '%prog' command removes internal Git data for projects that are no
+longer active in the current configuration.
+
+Projects excluded by the configured manifest groups are inactive by
+default. Use --keep-manifest-projects to keep Git data for projects that
+are still in the manifests.
+"""
 
     def _Options(self, p):
         p.add_option(
@@ -53,6 +61,12 @@
             help="repack all projects that use partial clone with "
             "filter=blob:none",
         )
+        p.add_option(
+            "--keep-manifest-projects",
+            default=False,
+            action="store_true",
+            help="keep Git data for projects still in the manifests",
+        )
 
     def _find_git_to_delete(
         self, to_keep: Set[str], start_dir: str
@@ -292,16 +306,21 @@
             args, all_manifests=not opt.this_manifest_only
         )
 
-        # If the user specified projects, fetch the global list separately
-        # to avoid deleting untargeted projects.
-        if args:
-            all_projects = self.GetProjects(
+        if opt.keep_manifest_projects:
+            projects_to_keep = self.GetProjects(
+                [],
+                groups="all",
+                missing_ok=True,
+                all_manifests=not opt.this_manifest_only,
+            )
+        elif args:
+            projects_to_keep = self.GetProjects(
                 [], all_manifests=not opt.this_manifest_only
             )
         else:
-            all_projects = projects
+            projects_to_keep = projects
 
-        ret = self.delete_unused_projects(all_projects, opt)
+        ret = self.delete_unused_projects(projects_to_keep, opt)
         if ret != 0:
             return ret
 
diff --git a/tests/test_subcmds_gc.py b/tests/test_subcmds_gc.py
index f5c415e..4aaa971 100644
--- a/tests/test_subcmds_gc.py
+++ b/tests/test_subcmds_gc.py
@@ -14,9 +14,11 @@
 
 """Unittests for the subcmds/gc.py module."""
 
+from pathlib import Path
 import unittest
 from unittest import mock
 
+import manifest_xml
 from subcmds import gc
 
 
@@ -80,3 +82,108 @@
         ret = self.cmd.Execute(self.opt, [])
         self.assertEqual(ret, 1)
         self.mock_repack.assert_not_called()
+
+
+def test_gc_keep_manifest_projects(tmp_path: Path) -> None:
+    """Keep inactive projects that are still in the manifest."""
+    repodir = tmp_path / ".repo"
+    manifest_dir = repodir / "manifests"
+    manifest_file = repodir / manifest_xml.MANIFEST_FILE_NAME
+
+    repodir.mkdir()
+    manifest_dir.mkdir()
+
+    manifest_gitdir = repodir / "manifests.git"
+    manifest_gitdir.mkdir()
+    (manifest_gitdir / "config").write_text(
+        """[remote "origin"]
+        url = https://localhost:0/manifest
+        """,
+        encoding="utf-8",
+    )
+
+    manifest_file.write_text(
+        """\
+        <manifest>
+        <remote name="origin" fetch="http://localhost" />
+        <default remote="origin" revision="refs/heads/main" />
+        <project name="included" groups="active-group" />
+        <project name="excluded" groups="other-group" />
+        </manifest>
+        """,
+        encoding="utf-8",
+    )
+
+    manifest = manifest_xml.XmlManifest(str(repodir), str(manifest_file))
+    manifest.manifestProject.config.SetString(
+        "manifest.groups",
+        "active-group",
+    )
+
+    projects = {project.name: project for project in manifest.projects}
+    included = projects["included"]
+    excluded = projects["excluded"]
+
+    Path(included.gitdir).mkdir(parents=True)
+    Path(included.objdir).mkdir(parents=True)
+
+    # Simulate an inactive project with only its object cache left.
+    Path(excluded.objdir).mkdir(parents=True)
+    assert not excluded.Exists
+
+    orphan_gitdir = repodir / "projects" / "orphan.git"
+    orphan_objdir = repodir / "project-objects" / "orphan.git"
+    orphan_gitdir.mkdir()
+    orphan_objdir.mkdir()
+
+    cmd = gc.Gc(repodir=str(repodir), manifest=manifest)
+
+    opt, args = cmd.OptionParser.parse_args(
+        ["--yes", "--keep-manifest-projects"]
+    )
+    opt.quiet = True
+
+    selected_projects = cmd.GetProjects([], all_manifests=True)
+    assert included in selected_projects
+    assert excluded not in selected_projects
+
+    cmd.Execute(opt, args)
+
+    assert included.Exists
+    assert Path(excluded.objdir).exists()
+    assert not orphan_gitdir.exists()
+    assert not orphan_objdir.exists()
+
+
+def test_gc_keep_manifest_projects_preserves_repack_targets() -> None:
+    """Keep manifest projects without expanding repack targets."""
+    cmd = gc.Gc()
+    opt, _ = cmd.OptionParser.parse_args(
+        ["--keep-manifest-projects", "--repack"]
+    )
+    opt.this_manifest_only = False
+
+    with mock.patch.object(
+        cmd,
+        "GetProjects",
+        side_effect=[["projA"], ["manifest_projects"]],
+    ) as get_projects, mock.patch.object(
+        cmd, "delete_unused_projects", return_value=0
+    ) as delete, mock.patch.object(
+        cmd, "repack_projects", return_value=0
+    ) as repack:
+        cmd.Execute(opt, ["projA"])
+
+    get_projects.assert_has_calls(
+        [
+            mock.call(["projA"], all_manifests=True),
+            mock.call(
+                [],
+                groups="all",
+                missing_ok=True,
+                all_manifests=True,
+            ),
+        ]
+    )
+    delete.assert_called_once_with(["manifest_projects"], opt)
+    repack.assert_called_once_with(["projA"], opt)