diff --git a/tools/build/mk/Makefile.boot b/tools/build/mk/Makefile.boot
index b4f13c2fcaf0..0b4c41b8d95f 100644
--- a/tools/build/mk/Makefile.boot
+++ b/tools/build/mk/Makefile.boot
@@ -8,12 +8,14 @@ LDFLAGS+=	-L${WORLDTMP}/legacy/usr/lib
 # we do not want to capture dependencies referring to the above
 UPDATE_DEPENDFILE= no
 
-.if !make(obj)
 # When building host tools we should never pull in headers from the source sys
 # directory to avoid any ABI issues that might cause the built binary to crash.
 # The only exceptions to this are sys/cddl/compat for dtrace bootstrap tools and
 # sys/crypto for libmd bootstrap.
-.if !empty(CFLAGS:M*${SRCTOP}/sys*:N*${SRCTOP}/sys/cddl/compat*:N*${SRCTOP}/sys/crypto*)
+# We have to skip this check during make obj since bsd.crunchgen.mk will run
+# make obj on every directory during the build-tools phase.
+.if !make(obj)
+.if !empty(CFLAGS:M*${SRCTOP}/sys)
 .error Do not include $${SRCTOP}/sys when building bootstrap tools. \
     Copy the header to $${WORLDTMP}/legacy in tools/build/Makefile instead. \
     Error was caused by Makefile in ${.CURDIR}