diff --git a/git-filter-branch.sh b/git-filter-branch.sh
index 98f1779cf..86b2ff1e0 100755
--- a/git-filter-branch.sh
+++ b/git-filter-branch.sh
@@ -404,7 +404,7 @@ while read commit parents; do
 	then
 		tree=$(git write-tree)
 	else
-		tree="$commit^{tree}"
+		tree=$(git rev-parse "$commit^{tree}")
 	fi
 	workdir=$workdir @SHELL_PATH@ -c "$filter_commit" "git commit-tree" \
 		"$tree" $parentstr < ../message > ../map/$commit ||
diff --git a/t/t7003-filter-branch.sh b/t/t7003-filter-branch.sh
index 8868e6e09..cb8fbd8e5 100755
--- a/t/t7003-filter-branch.sh
+++ b/t/t7003-filter-branch.sh
@@ -333,6 +333,14 @@ test_expect_success 'prune empty collapsed merges' '
 	test_cmp expect actual
 '
 
+test_expect_success 'prune empty works even without index/tree filters' '
+	git rev-list HEAD >expect &&
+	git commit --allow-empty -m empty &&
+	git filter-branch -f --prune-empty HEAD &&
+	git rev-list HEAD >actual &&
+	test_cmp expect actual
+'
+
 test_expect_success '--remap-to-ancestor with filename filters' '
 	git checkout master &&
 	git reset --hard A &&