diff --git a/pmb/chroot/__init__.py b/pmb/chroot/__init__.py
index 01ff116b..01b50a01 100644
--- a/pmb/chroot/__init__.py
+++ b/pmb/chroot/__init__.py
@@ -1,7 +1,7 @@
 # Copyright 2023 Oliver Smith
 # SPDX-License-Identifier: GPL-3.0-or-later
 from pmb.chroot.init import init, init_keys
-from pmb.chroot.mount import mount, mount_native_into_foreign
+from pmb.chroot.mount import mount, mount_native_into_foreign, remove_mnt_pmbootstrap
 from pmb.chroot.root import root
 from pmb.chroot.user import user
 from pmb.chroot.user import exists as user_exists
diff --git a/pmb/chroot/mount.py b/pmb/chroot/mount.py
index 65f00a7b..45053c0d 100644
--- a/pmb/chroot/mount.py
+++ b/pmb/chroot/mount.py
@@ -106,3 +106,18 @@ def mount_native_into_foreign(args, suffix):
     if not os.path.lexists(musl_link):
         pmb.helpers.run.root(args, ["ln", "-s", "/native/lib/" + musl,
                                     musl_link])
+
+def remove_mnt_pmbootstrap(args, suffix):
+    """ Safely remove /mnt/pmbootstrap directories from the chroot, without
+        running rm -r as root and potentially removing data inside the
+        mountpoint in case it was still mounted (bug in pmbootstrap, or user
+        ran pmbootstrap 2x in parallel). This is similar to running 'rm -r -d',
+        but we don't assume that the host's rm has the -d flag (busybox does
+        not). """
+    mnt_dir = f"{args.work}/chroot_{suffix}/mnt/pmbootstrap"
+
+    if not os.path.exists(mnt_dir):
+        return
+
+    for path in glob.glob(f"{mnt_dir}/*") + [mnt_dir]:
+        pmb.helpers.run.root(args, ["rmdir", path])
diff --git a/pmb/config/__init__.py b/pmb/config/__init__.py
index 2ded467a..12be7b1a 100644
--- a/pmb/config/__init__.py
+++ b/pmb/config/__init__.py
@@ -206,6 +206,7 @@ chroot_host_path = os.environ["PATH"] + ":/usr/sbin/"
 # $WORK gets replaced with args.work
 # $ARCH gets replaced with the chroot architecture (eg. x86_64, armhf)
 # $CHANNEL gets replaced with the release channel (e.g. edge, v21.03)
+# Use no more than one dir after /mnt/pmbootstrap, see remove_mnt_pmbootstrap.
 chroot_mount_bind = {
     "/proc": "/proc",
     "$WORK/cache_apk_$ARCH": "/var/cache/apk",
diff --git a/pmb/install/_install.py b/pmb/install/_install.py
index 4b7ff47c..98a9127e 100644
--- a/pmb/install/_install.py
+++ b/pmb/install/_install.py
@@ -816,6 +816,7 @@ def install_system_image(args, size_reserve, suffix, step, steps,
     # Clean up after running mkinitfs in chroot
     pmb.helpers.mount.umount_all(args, f"{args.work}/chroot_{suffix}")
     pmb.helpers.run.root(args, ["rm", f"{args.work}/chroot_{suffix}/in-pmbootstrap"])
+    pmb.chroot.remove_mnt_pmbootstrap(args, suffix)
 
     # Just copy all the files
     logging.info(f"*** ({step + 1}/{steps}) FILL INSTALL BLOCKDEVICE ***")
diff --git a/test/test_chroot_mount.py b/test/test_chroot_mount.py
new file mode 100644
index 00000000..2f4b66db
--- /dev/null
+++ b/test/test_chroot_mount.py
@@ -0,0 +1,40 @@
+# Copyright 2023 Oliver Smith
+# SPDX-License-Identifier: GPL-3.0-or-later
+""" Test pmb/chroot/mount.py """
+import os
+import pytest
+import sys
+
+import pmb_test  # noqa
+import pmb.chroot
+
+
+@pytest.fixture
+def args(tmpdir, request):
+    import pmb.parse
+    sys.argv = ["pmbootstrap", "init"]
+    args = pmb.parse.arguments()
+    args.log = args.work + "/log_testsuite.txt"
+    pmb.helpers.logging.init(args)
+    request.addfinalizer(pmb.helpers.logging.logfd.close)
+    return args
+
+
+def test_chroot_mount(args):
+    suffix = "native"
+    mnt_dir = f"{args.work}/chroot_native/mnt/pmbootstrap"
+
+    # Run something in the chroot to have the dirs created
+    pmb.chroot.root(args, ["true"])
+    assert os.path.exists(mnt_dir)
+    assert os.path.exists(f"{mnt_dir}/packages")
+
+    # Umount everything, like in pmb.install.install_system_image
+    pmb.helpers.mount.umount_all(args, f"{args.work}/chroot_{suffix}")
+
+    # Remove all /mnt/pmbootstrap dirs
+    pmb.chroot.remove_mnt_pmbootstrap(args, suffix)
+    assert not os.path.exists(mnt_dir)
+
+    # Run again: it should not crash
+    pmb.chroot.remove_mnt_pmbootstrap(args, suffix)