diff --git a/sdk_lib/make_chroot.sh b/sdk_lib/make_chroot.sh
index 5057aedfd2..9773349425 100755
--- a/sdk_lib/make_chroot.sh
+++ b/sdk_lib/make_chroot.sh
@@ -146,14 +146,6 @@ init_users () {
 
 init_setup () {
    info "Running init_setup()..."
-   mkdir -p -m 755 "${FLAGS_chroot}/usr" \
-     "${FLAGS_chroot}/usr/local/portage" \
-     "${FLAGS_chroot}"/"${CROSSDEV_OVERLAY}"
-   ln -sf "${CHROOT_TRUNK_DIR}/src/third_party/coreos-overlay" \
-     "${FLAGS_chroot}"/"${CHROOT_OVERLAY}"
-   ln -sf "${CHROOT_TRUNK_DIR}/src/third_party/portage-stable" \
-     "${FLAGS_chroot}"/"${PORTAGE_STABLE_OVERLAY}"
-
    # Set up sudoers.  Inside the chroot, the user can sudo without a password.
    # (Safe enough, since the only way into the chroot is to 'sudo chroot', so
    # the user's already typed in one sudo password...)
diff --git a/setup_board b/setup_board
index 4f65ddfc38..5f948fbe84 100755
--- a/setup_board
+++ b/setup_board
@@ -168,7 +168,8 @@ case "$BOARD" in
     ;;
 esac
 # Locations we will need
-COREOS_CONFIG="/usr/local/portage/coreos/coreos/config"
+COREOS_OVERLAY="${REPO_ROOT}/src/third_party/coreos-overlay"
+COREOS_CONFIG="${COREOS_OVERLAY}/coreos/config"
 BOARD_ROOT="/build/${BOARD_VARIANT}"
 BOARD_ETC="${BOARD_ROOT}/etc"
 BOARD_ARCH=$(get_board_arch "$BOARD")
diff --git a/update_chroot b/update_chroot
index 2d5c474db9..89abd6eb94 100755
--- a/update_chroot
+++ b/update_chroot
@@ -45,9 +45,9 @@ switch_to_strict_mode
 
 . "${BUILD_LIBRARY_DIR}/toolchain_util.sh"
 
-PORTAGE_STABLE_OVERLAY="/usr/local/portage/stable"
+PORTAGE_STABLE_OVERLAY="${REPO_ROOT}/src/third_party/portage-stable"
 CROSSDEV_OVERLAY="/usr/local/portage/crossdev"
-COREOS_OVERLAY="/usr/local/portage/coreos"
+COREOS_OVERLAY="${REPO_ROOT}/src/third_party/coreos-overlay"
 COREOS_CONFIG="${COREOS_OVERLAY}/coreos/config"
 
 info "Setting up portage..."