diff --git a/bin/omarchy-apply-pacman b/bin/omarchy-apply-pacman
index d5a92234..0af0fb0c 100755
--- a/bin/omarchy-apply-pacman
+++ b/bin/omarchy-apply-pacman
@@ -49,5 +49,6 @@ for file in pacman.conf pacman.d/mirrorlist; do
     cp -f "$etc/$file" "$etc/$file.bak"
   fi
 done
-install -m 644 "$staging/pacman.conf" "$etc/pacman.conf"
-install -m 644 "$staging/mirrorlist" "$etc/pacman.d/mirrorlist"
+# Copying over an existing file keeps its owner and mode, as refresh always has.
+cp -f "$staging/pacman.conf" "$etc/pacman.conf"
+cp -f "$staging/mirrorlist" "$etc/pacman.d/mirrorlist"
diff --git a/test/shell.d/region-pacman-test.sh b/test/shell.d/region-pacman-test.sh
index 92682e5e..2d0eb25a 100644
--- a/test/shell.d/region-pacman-test.sh
+++ b/test/shell.d/region-pacman-test.sh
@@ -18,6 +18,12 @@ for channel in stable rc edge; do
 done
 pass "missing region preserves all global channel templates byte for byte"
 
+chmod 600 "$TARGET_ROOT/etc/pacman.conf"
+apply stable
+[[ $(stat -c %a "$TARGET_ROOT/etc/pacman.conf") == 600 ]] || fail "refresh keeps a customized pacman.conf mode"
+chmod 644 "$TARGET_ROOT/etc/pacman.conf"
+pass "refresh keeps existing config file modes"
+
 printf 'cn\n' > "$TARGET_ROOT/etc/omarchy/region"
 for channel in stable rc edge; do
   case "$channel" in