diff --git a/tools/Makefile.host b/tools/Makefile.host
index 249b380c138..bb87ed91587 100644
--- a/tools/Makefile.host
+++ b/tools/Makefile.host
@@ -285,10 +285,10 @@ clean:
 	$(call DELFILE, nxstyle.exe)
 	$(call DELFILE, rmcr)
 	$(call DELFILE, rmcr.exe)
-	$(call DELFILE, incdir)
-	$(call DELFILE, incdir.exe)
 ifneq ($(CONFIG_WINDOWS_NATIVE),y)
 	$(Q) rm -rf *.dSYM
 endif
 	$(Q) $(MAKE) -C pic32 -f Makefile.host TOPDIR="$(TOPDIR)" clean
+	$(call DELFILE, incdir)
+	$(call DELFILE, incdir.exe)
 	$(call CLEAN)
diff --git a/tools/Makefile.unix b/tools/Makefile.unix
index f689d5c82b0..8a69b54ffc3 100644
--- a/tools/Makefile.unix
+++ b/tools/Makefile.unix
@@ -523,7 +523,6 @@ depend: pass1dep pass2dep
 $(foreach SDIR, $(CLEANDIRS), $(eval $(call SDIR_template,$(SDIR),clean)))
 
 subdir_clean: $(foreach SDIR, $(CLEANDIRS), $(SDIR)_clean)
-	$(Q) $(MAKE) -C tools -f Makefile.host TOPDIR="$(TOPDIR)" clean
 ifeq ($(CONFIG_BUILD_2PASS),y)
 	$(Q) $(MAKE) -C $(CONFIG_PASS1_BUILDIR) TOPDIR="$(TOPDIR)" clean
 endif
@@ -563,6 +562,7 @@ endif
 	$(Q) $(DIRUNLINK) $(ARCH_SRC)/board
 	$(Q) $(DIRUNLINK) $(ARCH_SRC)/chip
 	$(Q) $(DIRUNLINK) $(TOPDIR)/drivers/platform
+	$(Q) $(MAKE) -C tools -f Makefile.host TOPDIR="$(TOPDIR)" clean
 
 # Application housekeeping targets.  The APPDIR variable refers to the user
 # application directory.  A sample apps/ directory is included with NuttX,
diff --git a/tools/Makefile.win b/tools/Makefile.win
index fdc10cf4332..0d772316362 100644
--- a/tools/Makefile.win
+++ b/tools/Makefile.win
@@ -479,7 +479,6 @@ depend: pass1dep pass2dep
 $(foreach SDIR, $(CLEANDIRS), $(eval $(call SDIR_template,$(SDIR),clean)))
 
 subdir_clean: $(foreach SDIR, $(CLEANDIRS), $(SDIR)_clean)
-	$(Q) $(MAKE) -C tools -f Makefile.host TOPDIR="$(TOPDIR)" clean
 ifeq ($(CONFIG_BUILD_2PASS),y)
 	$(Q) $(MAKE) -C $(CONFIG_PASS1_BUILDIR) TOPDIR="$(TOPDIR)" clean
 endif
@@ -518,6 +517,7 @@ endif
 	$(call DIRUNLINK, $(ARCH_SRC)\board)
 	$(call DIRUNLINK, $(ARCH_SRC)\chip)
 	$(call DIRUNLINK, $(TOPDIR)\drivers\platform)
+	$(Q) $(MAKE) -C tools -f Makefile.host TOPDIR="$(TOPDIR)" clean
 
 # Application housekeeping targets.  The APPDIR variable refers to the user
 # application directory.  A sample apps\ directory is included with NuttX,