diff --git a/Makefile.in b/Makefile.in
index f28623ef565..253f7f7a54b 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -863,6 +863,7 @@ clean: $(clean_dirs:=_clean)
 	[ ! -d test ] || $(MAKE) -C test $@
 	-rm -f ./*.tmp etc/*.tmp*
 	-rm -rf info-dir.*
+	-rm -rf eln-cache
 
 ### 'bootclean'
 ###      Delete all files that need to be remade for a clean bootstrap.
diff --git a/lisp/Makefile.in b/lisp/Makefile.in
index 9bcceceb0ee..164e4a01f59 100644
--- a/lisp/Makefile.in
+++ b/lisp/Makefile.in
@@ -302,7 +302,7 @@ endif
 # subdirectories, to make sure require's and load's in the files being
 # compiled find the right files.
 
-.SUFFIXES: .eln .elc .el
+.SUFFIXES: .elc .el
 
 # An old-fashioned suffix rule, which, according to the GNU Make manual,
 # cannot have prerequisites.
@@ -357,13 +357,6 @@ compile-main: gen-lisp compile-clean
 		  TARGETS="$$chunk";		     \
 	done
 
-.PHONY: native-compile-clean
-native-compile-clean:
-# Erase all eln output compilation folders.
-ifeq ($(HAVE_NATIVE_COMP),yes)
-	find $(lisp) -regex ".*/eln-.*-[0-9a-z]+\\'" -type d | xargs rm -rf
-endif
-
 .PHONY: compile-clean
 # Erase left-over .elc files that do not have a corresponding .el file.
 compile-clean:
@@ -400,7 +393,7 @@ compile: $(LOADDEFS) autoloads compile-first
 # Compile all Lisp files.  This is like 'compile' but compiles files
 # unconditionally.  Some files don't actually get compiled because they
 # set the local variable no-byte-compile.
-compile-always: native-compile-clean
+compile-always:
 	find $(lisp) -name '*.elc' $(FIND_DELETE)
 	$(MAKE) compile
 
@@ -490,7 +483,7 @@ $(CAL_DIR)/hol-loaddefs.el: $(CAL_SRC) $(CAL_DIR)/diary-loaddefs.el
 
 .PHONY: bootstrap-clean distclean maintainer-clean extraclean
 
-bootstrap-clean: native-compile-clean
+bootstrap-clean:
 	find $(lisp) -name '*.elc' $(FIND_DELETE)
 	rm -f $(AUTOGENEL)
 
diff --git a/src/Makefile.in b/src/Makefile.in
index 63a4aa80e93..7380a87644b 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -790,10 +790,6 @@ tags: TAGS ../lisp/TAGS $(lwlibdir)/TAGS
 	@$(MAKE) $(AM_V_NO_PD) -C ../lisp EMACS="$(bootstrap_exe)"\
 		THEFILE=$< $<c
 
-%.eln: %.el | bootstrap-emacs$(EXEEXT) $(bootstrap_pdmp)
-	@$(MAKE)  $(AM_V_NO_PD) -C ../lisp EMACS="$(bootstrap_exe)"\
-		THEFILE=$< $<n
-
 ## VCSWITNESS points to the file that holds info about the current checkout.
 ## We use it as a heuristic to decide when to rebuild loaddefs.el.
 ## If empty it is ignored; the parent makefile can set it to some other value.