diff --git a/Kbuild b/Kbuild
index e122d93cee32..0b9e8a16a621 100644
--- a/Kbuild
+++ b/Kbuild
@@ -43,17 +43,32 @@ PHONY += missing-syscalls
 missing-syscalls: scripts/checksyscalls.sh $(offsets-file)
 	$(call cmd,syscalls)
 
-# Check atomic headers are up-to-date
+# Check the manual modification of atomic headers
 
-quiet_cmd_atomics = CALL    $<
-      cmd_atomics = $(CONFIG_SHELL) $<
+quiet_cmd_check_sha1 = CHKSHA1 $<
+      cmd_check_sha1 = \
+	if ! command -v sha1sum >/dev/null; then \
+		echo "warning: cannot check the header due to sha1sum missing"; \
+		exit 0; \
+	fi; \
+	if [ "$$(sed -n '$$s:// ::p' $<)" != \
+	     "$$(sed '$$d' $< | sha1sum | sed 's/ .*//')" ]; then \
+		echo "error: $< has been modified." >&2; \
+		exit 1; \
+	fi; \
+	touch $@
 
-PHONY += old-atomics
-old-atomics: scripts/atomic/check-atomics.sh
-	$(call cmd,atomics)
+atomic-checks += $(addprefix $(obj)/.checked-, \
+	  atomic-arch-fallback.h \
+	  atomic-instrumented.h \
+	  atomic-long.h)
+
+targets += $(atomic-checks)
+$(atomic-checks): $(obj)/.checked-%: include/linux/atomic/%  FORCE
+	$(call if_changed,check_sha1)
 
 # A phony target that depends on all the preparation targets
 
 PHONY += prepare
-prepare: $(offsets-file) missing-syscalls old-atomics
+prepare: $(offsets-file) missing-syscalls $(atomic-checks)
 	@:
diff --git a/Makefile b/Makefile
index a42b121d1cd5..22a4afd51285 100644
--- a/Makefile
+++ b/Makefile
@@ -1110,7 +1110,7 @@ vmlinux-dirs	:= $(patsubst %/,%,$(filter %/, \
 		     $(libs-y) $(libs-m)))
 
 build-dirs	:= $(vmlinux-dirs)
-clean-dirs	:= $(sort $(vmlinux-dirs) Documentation \
+clean-dirs	:= $(sort $(vmlinux-dirs) Documentation . \
 		     $(patsubst %/,%,$(filter %/, $(core-) \
 			$(drivers-) $(libs-))))
 
diff --git a/scripts/atomic/check-atomics.sh b/scripts/atomic/check-atomics.sh
deleted file mode 100755
index 0e7bab3eb0d1..000000000000
--- a/scripts/atomic/check-atomics.sh
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/bin/sh
-# SPDX-License-Identifier: GPL-2.0
-#
-# Check if atomic headers are up-to-date
-
-ATOMICDIR=$(dirname $0)
-ATOMICTBL=${ATOMICDIR}/atomics.tbl
-LINUXDIR=${ATOMICDIR}/../..
-
-echo '' | sha1sum - > /dev/null 2>&1
-if [ $? -ne 0 ]; then
-	printf "sha1sum not available, skipping atomic header checks.\n"
-	exit 0
-fi
-
-cat <<EOF |
-linux/atomic/atomic-instrumented.h
-linux/atomic/atomic-long.h
-linux/atomic/atomic-arch-fallback.h
-EOF
-while read header; do
-	OLDSUM="$(tail -n 1 ${LINUXDIR}/include/${header})"
-	OLDSUM="${OLDSUM#// }"
-
-	NEWSUM="$(sed '$d' ${LINUXDIR}/include/${header} | sha1sum)"
-	NEWSUM="${NEWSUM%% *}"
-
-	if [ "${OLDSUM}" != "${NEWSUM}" ]; then
-		printf "warning: generated include/${header} has been modified.\n"
-	fi
-done
-
-exit 0