diff --git a/Makefile.am.inc b/Makefile.am.inc
index 5a107689e7..9bf5cf87d2 100644
--- a/Makefile.am.inc
+++ b/Makefile.am.inc
@@ -44,6 +44,11 @@ am__v_SED_0 = @echo "  SED     " $@;
 	$(AM_V_AWK)$(AWK) '/^EXPORTS$$/ {next;}; ${def_sym_filter_symbols} /^[^;]/ { print $$1;}' < $< > $@
 
 # abi-compliance-checker descriptor
-INCLUDE_DIRS = $(subst -I,NEWLINE,$(filter -I%, $(CFLAGS) -I$(abs_top_srcdir) -I$(abs_srcdir)))
+abi_incdirs = $(subst -I,NEWLINE,$(filter -I%,$(CFLAGS) -I$(abs_top_srcdir) -I$(abs_srcdir)))
+abi_sysdirs = $(subst -isystem,NEWLINE,$(filter -isystem%,$(CFLAGS)))
+INCLUDE_DIRS = $(abi_incdirs) $(abi_sysdirs)
 abi-descriptor.xml: ../abi-descriptor.template
-	$(AM_V_SED)sed "s|@INCLUDE_DIRS@|$(INCLUDE_DIRS)|g;s/NEWLINE/\n    /g;s|@LIBRARY_OUTPUT_PATH@|{RELPATH}/.libs|" $< > $@
+	$(AM_V_SED)sed \
+		-e 's|@INCLUDE_DIRS@|$(INCLUDE_DIRS)|g' \
+		-e 's/ *NEWLINE/\n    /g' \
+		-e 's|@LIBRARY_OUTPUT_PATH@|{RELPATH}/.libs|' $< > $@
diff --git a/abi-descriptor.template b/abi-descriptor.template
index 43dd9a6fd6..8f1be3e52e 100644
--- a/abi-descriptor.template
+++ b/abi-descriptor.template
@@ -1,20 +1,20 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <descriptor>
-<version>
+  <version>
     0.0.0
-</version>
-<headers>
+  </version>
+  <headers>
     {RELPATH}/abi-check-headers
-</headers>
-<libs>
+  </headers>
+  <libs>
     @LIBRARY_OUTPUT_PATH@
-</libs>
-<include_paths>@INCLUDE_DIRS@
-</include_paths>
-<gcc_options>
+  </libs>
+  <include_paths>@INCLUDE_DIRS@
+  </include_paths>
+  <gcc_options>
     -D_U_="__attribute((unused))"
-</gcc_options>
-<include_preamble>
+  </gcc_options>
+  <include_preamble>
     config.h
-</include_preamble>
+  </include_preamble>
 </descriptor>