diff --git a/dotdrop/updater.py b/dotdrop/updater.py
index e482237c..8745db39 100644
--- a/dotdrop/updater.py
+++ b/dotdrop/updater.py
@@ -258,6 +258,21 @@ def _handle_file(self, deployed_path, local_path,
             return False
         return True
 
+    def _prune_nested_paths(self, entries):
+        """return only top-most paths to avoid redundant removals"""
+        pruned = []
+        kept = set()
+        normalized = [entry.rstrip(os.path.sep) for entry in entries]
+        for entry in sorted(normalized, key=lambda x: x.count(os.path.sep)):
+            if any(
+                entry == k or entry.startswith(k + os.path.sep)
+                for k in kept
+            ):
+                continue
+            kept.add(entry)
+            pruned.append(entry)
+        return pruned
+
     def _handle_dir(self, deployed_path, local_path,
                     dotfile, ignores):
         """sync path (local dir) and local_path (dotdrop dir path)"""
@@ -277,6 +292,7 @@ def _handle_dir(self, deployed_path, local_path,
         lonly, ronly, common = local_tree.compare(deploy_tree)
 
         # those only in dotpath
+        lonly = self._prune_nested_paths(lonly)
         for i in lonly:
             path = os.path.join(local_path, i)
             if self.dry:
diff --git a/tests-ng/update-prune-nested-remove.sh b/tests-ng/update-prune-nested-remove.sh
new file mode 100755
index 00000000..446efd7b
--- /dev/null
+++ b/tests-ng/update-prune-nested-remove.sh
@@ -0,0 +1,81 @@
+#!/usr/bin/env bash
+# author: deadc0de6 (https://github.com/deadc0de6)
+# Copyright (c) 2026, deadc0de6
+#
+# ensure update prunes nested removals
+# 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)
+dotpath="${basedir}/dotfiles"
+
+# deployed directory
+deployed=$(mktemp -d --suffix='-dotdrop-fs' || mktemp -d)
+rel_deployed="${deployed#/}"
+
+# misc files to cleanup
+outlog=$(mktemp -t dotdrop-update-XXXX || mktemp)
+
+clear_on_exit "${basedir}"
+clear_on_exit "${deployed}"
+clear_on_exit "${outlog}"
+
+# create the config file
+cfg="${basedir}/config.yaml"
+create_conf "${cfg}"
+
+# create deployed content
+mkdir -p "${deployed}/sub"
+echo 'config' > "${deployed}/config.yaml"
+echo 'style' > "${deployed}/style.css"
+echo 'test' > "${deployed}/sub/test"
+
+# import the directory
+cd "${ddpath}" | ${bin} import -f -c "${cfg}" "${deployed}"
+
+# remove the nested directory on the filesystem
+rm -rf "${deployed}/sub"
+
+# update dotpath and capture output
+cd "${ddpath}" | ${bin} update -f --verbose -c "${cfg}" "${deployed}" | tee "${outlog}"
+
+# ensure sub removed from dotpath
+[ -d "${dotpath}/${rel_deployed}/sub" ] && echo "sub directory not removed from dotpath" && exit 1
+[ -e "${dotpath}/${rel_deployed}/sub/test" ] && echo "nested file still present in dotpath" && exit 1
+
+# ensure only top-level removal is logged once
+count_sub=$( (grep -F "\"${dotpath}/${rel_deployed}/sub\" removed" "${outlog}" || true) | wc -l | tr -d ' ')
+count_sub_slash=$( (grep -F "\"${dotpath}/${rel_deployed}/sub/\" removed" "${outlog}" || true) | wc -l | tr -d ' ')
+count_nested=$( (grep -F "\"${dotpath}/${rel_deployed}/sub/test\" removed" "${outlog}" || true) | wc -l | tr -d ' ')
+count_nested_slash=$( (grep -F "\"${dotpath}/${rel_deployed}/sub/test/\" removed" "${outlog}" || true) | wc -l | tr -d ' ')
+
+total_sub=$((count_sub + count_sub_slash))
+[ "${total_sub}" -ne 1 ] && echo "expected single removal of sub directory, got ${total_sub}" && exit 1
+
+total_nested=$((count_nested + count_nested_slash))
+[ "${total_nested}" -ne 0 ] && echo "unexpected nested removal logged" && exit 1
+
+echo "OK"
+exit 0