diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 6df0a99184..6993d5ae1a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,8 +1,8 @@
 stages:
   - style-check
   - build
-  - flatpak
   - deploy
+  - flatpak
 
 .cache-paths: &cache-paths
   paths:
@@ -175,9 +175,9 @@ pages:
     - meson ${COMMON_MESON_FLAGS} -Dgtk_doc=true _build
     - ninja -C _build gdk4-doc gsk4-doc gtk4-doc
     - mkdir -p public/
-    - mv _build/docs/reference/gtk/html/ public/gtk/
     - mv _build/docs/reference/gdk/html/ public/gdk/
     - mv _build/docs/reference/gsk/html/ public/gsk/
+    - mv _build/docs/reference/gtk/html/ public/gtk/
   artifacts:
     paths:
       - public
diff --git a/.gitlab-ci/flatpak-build.sh b/.gitlab-ci/flatpak-build.sh
index 7b9464d130..9b27b6290e 100644
--- a/.gitlab-ci/flatpak-build.sh
+++ b/.gitlab-ci/flatpak-build.sh
@@ -4,7 +4,7 @@ set -e
 
 appid=$1
 
-builddir=app
+builddir=flatpak_app
 repodir=repo
 
 flatpak-builder \
@@ -12,12 +12,10 @@ flatpak-builder \
         ${builddir} \
         build-aux/flatpak/${appid}.json
 
-flatpak-builder \
-        --run ${builddir} build-aux/flatpak/${appid}.json \
-        meson \
-                --prefix /app \
-                --libdir /app/lib \
-                --buildtype release \
+flatpak build ${builddir} meson \
+                --prefix=/app \
+                --libdir=/app/lib \
+                --buildtype=release \
                 -Dx11-backend=true \
                 -Dwayland-backend=true \
                 -Dprint-backends=file \
@@ -27,9 +25,7 @@ flatpak-builder \
                 -Ddemos=true \
                 _build .
 
-flatpak-builder \
-        --run ${builddir} build-aux/flatpak/${appid}.json \
-        ninja -C _build install
+flatpak build ${builddir} ninja -C _build install
 
 flatpak-builder \
         --finish-only \
@@ -40,5 +36,5 @@ flatpak-builder \
 flatpak build-bundle \
         ${repodir} \
         ${appid}-dev.flatpak \
-        --runtime-repo=https://flathub.org/repo/flathub.flatpakrepo \
+        --runtime-repo=https://nightly.gnome.org/gnome-nightly.flatpakrepo \
         ${appid}
diff --git a/.gitlab-ci/run-tests.sh b/.gitlab-ci/run-tests.sh
index 9bac5b93c8..5638fa6593 100755
--- a/.gitlab-ci/run-tests.sh
+++ b/.gitlab-ci/run-tests.sh
@@ -17,16 +17,18 @@ xvfb-run -a -s "-screen 0 1024x768x24" \
 # generate the reports
 exit_code=$?
 
+cd ${builddir}
+
 $srcdir/.gitlab-ci/meson-junit-report.py \
         --project-name=gtk \
         --job-id="${CI_JOB_NAME}" \
-        --output=${builddir}/report.xml \
-        ${builddir}/meson-logs/testlog.json
+        --output=report.xml \
+        meson-logs/testlog.json
 $srcdir/.gitlab-ci/meson-html-report.py \
         --project-name=gtk \
         --job-id="${CI_JOB_NAME}" \
-        --reftest-output-dir="${builddir}/testsuite/reftests/output" \
-        --output=${builddir}/report.html \
-        ${builddir}/meson-logs/testlog.json
+        --reftest-output-dir="testsuite/reftests/output" \
+        --output=report.html \
+        meson-logs/testlog.json
 
 exit $exit_code