diff --git a/docs/usage.md b/docs/usage.md
index 557661c2..aea0f74d 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -102,7 +102,7 @@ Some available options:
 * `-a`/`--force-actions`: Force the execution of actions even if the dotfiles are not installed (see [Fake dotfile and actions](config/config-actions.md#fake-dotfile-and-actions) as an alternative)
 * `-f`/`--force`: Do not ask for any confirmation
 * `-W`/`--workdir-clear`: Clear the `workdir` before installing dotfiles (see [the config entry](config/config-config.md) `clear_workdir`)
-* `-R`/`remove-existing`: Applies to directory dotfiles only (`nolink`) and will remove files not managed by dotdrop in the destination directory
+* `-R`/`--remove-existing`: Applies to directory dotfiles. With `link: nolink`, it removes files not managed by dotdrop in the destination directory. With `link: link_children`, it removes only dangling direct-child symlinks whose source child no longer exists and whose target is inside the dotfile's source directory or dotdrop's `workdir`; other destination entries are preserved.
 
 To ignore specific patterns during installation, see [the ignore patterns](config/config-file.md#ignore-patterns).
 
diff --git a/dotdrop/installer.py b/dotdrop/installer.py
index d3233bf0..98d84d1a 100644
--- a/dotdrop/installer.py
+++ b/dotdrop/installer.py
@@ -406,6 +406,8 @@ def _link_children(self, templater, src, dst,
             self._create_dirs(dst)
 
         children = os.listdir(parent)
+        if self.remove_existing_in_dir:
+            self._remove_stale_link_children(parent, dst)
         srcs = [os.path.normpath(os.path.join(parent, child))
                 for child in children]
         dsts = [os.path.normpath(os.path.join(dst, child))
@@ -704,6 +706,44 @@ def _remove_existing_in_dir(self, directory, installed_files=None):
             if not removepath(path, logger=self.log):
                 self.log.warn(f'unable to remove {path}')
 
+    def _remove_stale_link_children(self, source, destination):
+        """remove stale links previously installed by link_children"""
+        if not os.path.isdir(destination):
+            return
+        managed_roots = [os.path.realpath(source),
+                         os.path.realpath(self.workdir)]
+        for child in os.listdir(destination):
+            if os.path.lexists(os.path.join(source, child)):
+                continue
+            path = os.path.join(destination, child)
+            if not self._is_managed_dangling_link(path, managed_roots):
+                continue
+
+            if self.dry:
+                self.log.dry(f'would remove stale link "{path}"')
+                continue
+            if self.safe and not self.log.ask(f'remove stale link "{path}"'):
+                return
+            if not removepath(path, logger=self.log):
+                self.log.warn(f'unable to remove {path}')
+                continue
+            self.log.sub(f'removed stale link "{path}"')
+
+    @staticmethod
+    def _is_managed_dangling_link(path, managed_roots):
+        """return true for a dangling link into a managed directory"""
+        if not os.path.islink(path) or os.path.exists(path):
+            return False
+        target = os.path.join(os.path.dirname(path), os.readlink(path))
+        target = os.path.realpath(target)
+        for root in managed_roots:
+            try:
+                if os.path.commonpath([target, root]) == root:
+                    return True
+            except ValueError:
+                continue
+        return False
+
     @classmethod
     def _write_content_to_file(cls, content, src, dst):
         """write content to file"""
diff --git a/dotdrop/options.py b/dotdrop/options.py
index ca14e225..1769a91a 100644
--- a/dotdrop/options.py
+++ b/dotdrop/options.py
@@ -96,7 +96,7 @@
   -n --nodiff             Do not diff when installing.
   -p --profile=<profile>  Specify the profile to use [default: {PROFILE}].
   -P --show-patch         Provide a one-liner to manually patch template.
-  -R --remove-existing    Remove existing file on install directory.
+  -R --remove-existing    Remove stale entries from installed directories.
   -s --as=<path>          Import as a different path from actual path.
   --transr=<key>          Associate trans_install key on import.
   --transw=<key>          Apply trans_update key on import.
diff --git a/tests-ng/install-link-children-remove-existing.sh b/tests-ng/install-link-children-remove-existing.sh
new file mode 100755
index 00000000..29b8b26b
--- /dev/null
+++ b/tests-ng/install-link-children-remove-existing.sh
@@ -0,0 +1,91 @@
+#!/usr/bin/env bash
+# author: deadc0de6 (https://github.com/deadc0de6)
+# Copyright (c) 2026, deadc0de6
+#
+# test removing stale links installed with link_children
+# returns 1 in case of error
+#
+
+## start-cookie
+set -eu -o errtrace -o pipefail
+cur=$(cd "$(dirname "${0}")" && pwd)
+ddpath="${cur}/../"
+PPATH="{PYTHONPATH:-}"
+export PYTHONPATH="${ddpath}:${PPATH}"
+altbin="python3 -m dotdrop.dotdrop"
+if hash coverage 2>/dev/null; then
+  mkdir -p coverages/
+  altbin="coverage run -p --data-file coverages/coverage --source=dotdrop -m dotdrop.dotdrop"
+fi
+bin="${DT_BIN:-${altbin}}"
+# shellcheck source=tests-ng/helpers
+source "${cur}"/helpers
+echo -e "$(tput setaf 6)==> RUNNING $(basename "${BASH_SOURCE[0]}") <==$(tput sgr0)"
+## end-cookie
+
+################################################################
+# this is the test
+################################################################
+
+# dotdrop directory
+basedir=$(mktemp -d --suffix='-dotdrop-tests' || mktemp -d)
+source_dir="${basedir}/dotfiles/skills"
+
+# deployed directory
+destination=$(mktemp -d --suffix='-dotdrop-fs' || mktemp -d)
+
+clear_on_exit "${basedir}"
+clear_on_exit "${destination}"
+
+# create the config file
+cfg="${basedir}/config.yaml"
+cat > "${cfg}" << _EOF
+config:
+  backup: true
+  create: true
+  dotpath: dotfiles
+dotfiles:
+  d_skills:
+    src: skills
+    dst: ${destination}
+    link: link_children
+    template: false
+profiles:
+  p1:
+    dotfiles:
+    - d_skills
+_EOF
+
+# create managed and unmanaged destination entries
+mkdir -p "${source_dir}/kept-skill"
+mkdir -p "${source_dir}/removed-skill"
+mkdir -p "${destination}/.system"
+echo 'local' > "${destination}/local-file"
+ln -s "${basedir}/unrelated-missing" "${destination}/unrelated-link"
+
+# install the managed links
+cd "${ddpath}" | ${bin} install -f -c "${cfg}" -p p1
+[ ! -h "${destination}/kept-skill" ] && echo "kept-skill not linked" && exit 1
+[ ! -h "${destination}/removed-skill" ] && echo "removed-skill not linked" && exit 1
+
+# remove one source child and ensure pruning remains opt-in
+rm -rf "${source_dir}/removed-skill"
+cd "${ddpath}" | ${bin} install -f -c "${cfg}" -p p1
+[ ! -h "${destination}/removed-skill" ] && echo "stale link removed without opt-in" && exit 1
+
+# dry run must report the stale link without removing it
+out=$(cd "${ddpath}" | ${bin} install --remove-existing --dry -f -c "${cfg}" -p p1)
+echo "${out}"
+echo "${out}" | grep -F "would remove stale link \"${destination}/removed-skill\"" >/dev/null
+[ ! -h "${destination}/removed-skill" ] && echo "stale link removed during dry run" && exit 1
+
+# remove only the stale managed link
+cd "${ddpath}" | ${bin} install --remove-existing -f -c "${cfg}" -p p1
+[ -h "${destination}/removed-skill" ] && echo "stale link not removed" && exit 1
+[ ! -h "${destination}/kept-skill" ] && echo "live link removed" && exit 1
+[ ! -h "${destination}/unrelated-link" ] && echo "unrelated link removed" && exit 1
+[ ! -d "${destination}/.system" ] && echo "local directory removed" && exit 1
+[ ! -f "${destination}/local-file" ] && echo "local file removed" && exit 1
+
+echo "OK"
+exit 0
diff --git a/tests/test_install.py b/tests/test_install.py
index 11afbc6d..1b36977a 100644
--- a/tests/test_install.py
+++ b/tests/test_install.py
@@ -6,7 +6,7 @@
 
 import os
 import unittest
-from unittest.mock import MagicMock
+from unittest.mock import MagicMock, call
 import filecmp
 from tests.helpers import (clean, create_dir, create_fake_config,
                            create_random_file, get_string, get_tempdir,
@@ -389,6 +389,105 @@ def test_link_children(self):
             xyz = os.path.join(dst_dir, src)
             self.assertEqual(os.path.realpath(xyz), os.path.realpath(src))
 
+    def test_link_children_remove_existing(self):
+        """test pruning stale links created by link_children"""
+        source = get_tempdir()
+        destination = get_tempdir()
+        workdir = get_tempdir()
+        self.addCleanup(clean, source)
+        self.addCleanup(clean, destination)
+        self.addCleanup(clean, workdir)
+
+        source_file, _ = create_random_file(source)
+        declared_broken = os.path.join(source, 'declared-broken')
+        os.symlink('missing', declared_broken)
+
+        stale = {
+            'source-absolute': os.path.join(source, 'missing-absolute'),
+            'source-relative': os.path.relpath(
+                os.path.join(source, 'missing-relative'), destination),
+            'workdir-absolute': os.path.join(workdir, 'missing-absolute'),
+            'workdir-relative': os.path.relpath(
+                os.path.join(workdir, 'missing-relative'), destination),
+        }
+        stale_paths = []
+        for name, target in stale.items():
+            path = os.path.join(destination, name)
+            os.symlink(target, path)
+            stale_paths.append(path)
+
+        regular = os.path.join(destination, 'regular')
+        with open(regular, 'w', encoding='utf-8') as file:
+            file.write('preserve')
+        directory = os.path.join(destination, 'directory')
+        os.mkdir(directory)
+        nested = os.path.join(directory, 'nested-stale')
+        os.symlink(os.path.join(source, 'missing-nested'), nested)
+        live = os.path.join(destination, 'live')
+        os.symlink(source_file, live)
+        unrelated = os.path.join(destination, 'unrelated')
+        os.symlink(os.path.join(source + '-other', 'missing'), unrelated)
+        declared = os.path.join(destination, 'declared-broken')
+        os.symlink(declared_broken, declared)
+
+        installer = Installer(workdir=workdir,
+                              remove_existing_in_dir=True)
+        installer.log.sub = MagicMock()
+        installer.install(templater=MagicMock(), src=source,
+                          dst=destination,
+                          linktype=LinkTypes.LINK_CHILDREN,
+                          actionexec=None, is_template=False)
+
+        for path in stale_paths:
+            self.assertFalse(os.path.lexists(path))
+        for path in [regular, directory, nested, live, unrelated, declared]:
+            self.assertTrue(os.path.lexists(path))
+        expected = [call(f'removed stale link "{path}"')
+                    for path in stale_paths]
+        installer.log.sub.assert_has_calls(expected, any_order=True)
+
+    def test_link_children_remove_existing_is_opt_in(self):
+        """test link_children pruning is disabled by default"""
+        source = get_tempdir()
+        destination = get_tempdir()
+        workdir = get_tempdir()
+        self.addCleanup(clean, source)
+        self.addCleanup(clean, destination)
+        self.addCleanup(clean, workdir)
+        stale = os.path.join(destination, 'stale')
+        os.symlink(os.path.join(source, 'missing'), stale)
+
+        installer = Installer(workdir=workdir)
+        installer.install(templater=MagicMock(), src=source,
+                          dst=destination,
+                          linktype=LinkTypes.LINK_CHILDREN,
+                          actionexec=None, is_template=False)
+
+        self.assertTrue(os.path.lexists(stale))
+
+    def test_link_children_remove_existing_dry(self):
+        """test dry link_children pruning is reported but not applied"""
+        source = get_tempdir()
+        destination = get_tempdir()
+        workdir = get_tempdir()
+        self.addCleanup(clean, source)
+        self.addCleanup(clean, destination)
+        self.addCleanup(clean, workdir)
+        stale = os.path.join(destination, 'stale')
+        os.symlink(os.path.join(source, 'missing'), stale)
+
+        installer = Installer(workdir=workdir, dry=True,
+                              remove_existing_in_dir=True)
+        installer.log.dry = MagicMock()
+        installer.install(templater=MagicMock(), src=source,
+                          dst=destination,
+                          linktype=LinkTypes.LINK_CHILDREN,
+                          actionexec=None, is_template=False)
+
+        self.assertTrue(os.path.lexists(stale))
+        installer.log.dry.assert_called_once_with(
+            f'would remove stale link "{stale}"')
+
     def test_fails_without_src(self):
         """test fails without src"""
         src = '/some/non/existant/file'