diff --git a/Makefile.am b/Makefile.am
index 2b94cb64..b005fd31 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -102,8 +102,6 @@ src_iwd_SOURCES = src/main.c linux/nl80211.h \
 
 src_iwd_LDADD = ell/libell-internal.la -ldl
 
-dist_sysconf_DATA = src/main.conf
-
 client_iwctl_SOURCES = client/main.c \
 			client/adapter.c \
 			client/agent-manager.c \
@@ -267,7 +265,7 @@ if BUILD_DOCS
 dist_man_MANS = $(manual_pages)
 endif
 
-EXTRA_DIST = src/genbuiltin $(manual_pages:.1=.txt)
+EXTRA_DIST = src/genbuiltin doc/main.conf $(manual_pages:.1=.txt)
 
 AM_CFLAGS = -fvisibility=hidden
 
diff --git a/bootstrap-configure b/bootstrap-configure
index a5b45159..22e6a389 100755
--- a/bootstrap-configure
+++ b/bootstrap-configure
@@ -7,7 +7,6 @@ fi
 ./bootstrap && \
     ./configure --enable-maintainer-mode \
 		--enable-debug \
+		--prefix=/usr \
 		--localstatedir=/var \
-		--prefix=/usr $* \
-		--sysconfdir=/etc/iwd \
-		--with-dbusconfdir=/etc
+		--with-dbusconfdir=/etc $*
diff --git a/src/main.conf b/doc/main.conf
similarity index 100%
rename from src/main.conf
rename to doc/main.conf