diff --git a/meta/conf/bitbake.conf b/meta/conf/bitbake.conf
index a85fea77..89b3e6a3 100644
--- a/meta/conf/bitbake.conf
+++ b/meta/conf/bitbake.conf
@@ -97,8 +97,8 @@ REPO_ISAR_DB_DIR = "${DEPLOY_DIR}/isar-apt/${DISTRO}-${DISTRO_ARCH}/db"
 THIRD_PARTY_APT_KEYRING = "/etc/apt/trusted.gpg.d/third_party.gpg"
 
 # Base apt repository paths
-REPO_BASE_DIR = "${DEPLOY_DIR}/base-apt/${DISTRO}/apt"
-REPO_BASE_DB_DIR = "${DEPLOY_DIR}/base-apt/${DISTRO}/db"
+REPO_BASE_DIR = "${TOPDIR}/base-apt/${DISTRO}/apt"
+REPO_BASE_DB_DIR = "${TOPDIR}/base-apt/${DISTRO}/db"
 
 # Setup our default hash policy
 BB_SIGNATURE_HANDLER ?= "OEBasicHash"
diff --git a/testsuite/citest.py b/testsuite/citest.py
index 17a90244..2393e275 100755
--- a/testsuite/citest.py
+++ b/testsuite/citest.py
@@ -86,9 +86,11 @@ class ReproTest(CIBaseTest):
 
         self.init()
         try:
+            self.delete_from_build_dir('base-apt')
             self.perform_repro_test(targets, signed=True)
         finally:
             self.move_in_build_dir('tmp', 'tmp_repro_signed')
+            self.move_in_build_dir('base-apt', 'base-apt_repro_signed')
 
     def test_repro_unsigned(self):
         targets = [
@@ -101,6 +103,7 @@ class ReproTest(CIBaseTest):
             self.perform_repro_test(targets, cross=False)
         finally:
             self.move_in_build_dir('tmp', 'tmp_repro_unsigned')
+            self.move_in_build_dir('base-apt', 'base-apt_repro_unsigned')
 
 class CcacheTest(CIBaseTest):