diff --git a/tools/perf/Makefile b/tools/perf/Makefile
index 41abb90df50d..dcb9700b88d2 100644
--- a/tools/perf/Makefile
+++ b/tools/perf/Makefile
@@ -157,10 +157,6 @@ all::
 #
 # Define NO_DWARF if you do not want debug-info analysis feature at all.
 
-$(shell sh -c 'mkdir -p $(OUTPUT)scripts/{perl,python}/Perf-Trace-Util/' 2> /dev/null)
-$(shell sh -c 'mkdir -p $(OUTPUT)util/{ui/browsers,scripting-engines}/' 2> /dev/null)
-$(shell sh -c 'mkdir $(OUTPUT)bench' 2> /dev/null)
-
 $(OUTPUT)PERF-VERSION-FILE: .FORCE-PERF-VERSION-FILE
 	@$(SHELL_PATH) util/PERF-VERSION-GEN $(OUTPUT)
 -include $(OUTPUT)PERF-VERSION-FILE
@@ -186,8 +182,6 @@ ifeq ($(ARCH),x86_64)
         ARCH := x86
 endif
 
-$(shell sh -c 'mkdir -p $(OUTPUT)arch/$(ARCH)/util/' 2> /dev/null)
-
 # CFLAGS and LDFLAGS are for the users to override from the command line.
 
 #
@@ -268,6 +262,7 @@ export prefix bindir sharedir sysconfdir
 CC = $(CROSS_COMPILE)gcc
 AR = $(CROSS_COMPILE)ar
 RM = rm -f
+MKDIR = mkdir
 TAR = tar
 FIND = find
 INSTALL = install
@@ -838,6 +833,7 @@ ifndef V
 	QUIET_CC       = @echo '   ' CC $@;
 	QUIET_AR       = @echo '   ' AR $@;
 	QUIET_LINK     = @echo '   ' LINK $@;
+	QUIET_MKDIR    = @echo '   ' MKDIR $@;
 	QUIET_BUILT_IN = @echo '   ' BUILTIN $@;
 	QUIET_GEN      = @echo '   ' GEN $@;
 	QUIET_SUBDIR0  = +@subdir=
@@ -1012,6 +1008,14 @@ $(LIB_OBJS) $(BUILTIN_OBJS): $(LIB_H)
 $(patsubst perf-%$X,%.o,$(PROGRAMS)): $(LIB_H) $(wildcard */*.h)
 builtin-revert.o wt-status.o: wt-status.h
 
+# we compile into subdirectories. if the target directory is not the source directory, they might not exists. So
+# we depend the various files onto their directories.
+DIRECTORY_DEPS = $(LIB_OBJS) $(BUILTIN_OBJS) $(OUTPUT)PERF-VERSION-FILE $(OUTPUT)common-cmds.h
+$(DIRECTORY_DEPS): $(sort $(dir $(DIRECTORY_DEPS)))
+# In the second step, we make a rule to actually create these directories
+$(sort $(dir $(DIRECTORY_DEPS))):
+	$(QUIET_MKDIR)$(MKDIR) -p $@ 2>/dev/null
+
 $(LIB_FILE): $(LIB_OBJS)
 	$(QUIET_AR)$(RM) $@ && $(AR) rcs $@ $(LIB_OBJS)