diff --git a/projects/scripts/project-altera.mk b/projects/scripts/project-altera.mk
index 48eeda960..ae7a24f68 100644
--- a/projects/scripts/project-altera.mk
+++ b/projects/scripts/project-altera.mk
@@ -42,6 +42,9 @@ CLEAN_TARGET +=  *.jdi
 CLEAN_TARGET += *.pin
 CLEAN_TARGET += *_summary.csv
 CLEAN_TARGET += *.dpf
+CLEAN_TARGET += system_qsys_script.tcl
+CLEAN_TARGET += system_bd.qsys
+CLEAN_TARGET += .qsys_edit
 
 M_DEPS += system_top.v
 M_DEPS += system_qsys.tcl
diff --git a/projects/scripts/project-xilinx.mk b/projects/scripts/project-xilinx.mk
index 0d1a2e41a..5c3b8f294 100644
--- a/projects/scripts/project-xilinx.mk
+++ b/projects/scripts/project-xilinx.mk
@@ -21,6 +21,7 @@ CLEAN_TARGET += *.hw
 CLEAN_TARGET += *.sim
 CLEAN_TARGET += .Xil
 CLEAN_TARGET += *.ip_user_files
+CLEAN_TARGET += *.str
 
 # Common dependencies that all projects have
 M_DEPS += system_project.tcl