diff --git a/config/ChangeLog b/config/ChangeLog
index 258dcb128f2049c236f616f5c14e31029eb5f5fc..37456f9fcafd5a61fbd00d2697acbf1056441a2c 100644
--- a/config/ChangeLog
+++ b/config/ChangeLog
@@ -1,3 +1,7 @@
+2019-04-16  Martin Liska  <mliska@suse.cz>
+
+	* bootstrap-lto-lean.mk: Filter out -flto in STAGEtrain_CFLAGS.
+
 2019-04-09  Martin Liska  <mliska@suse.cz>
 
 	* bootstrap-lto-lean.mk: New file.
diff --git a/config/bootstrap-lto-lean.mk b/config/bootstrap-lto-lean.mk
index ee36f6fe54415a7d31b4c013607a197a430119cb..79cea50a4c64c22140fd5009350d2a525748dc61 100644
--- a/config/bootstrap-lto-lean.mk
+++ b/config/bootstrap-lto-lean.mk
@@ -2,6 +2,7 @@
 # Otherwise, LTO is used in only stage3.
 
 STAGE3_CFLAGS += -flto=jobserver
+override STAGEtrain_CFLAGS := $(filter-out -flto=jobserver,$(STAGEtrain_CFLAGS))
 STAGEtrain_GENERATOR_CFLAGS += -flto=jobserver
 STAGEfeedback_CFLAGS += -flto=jobserver