diff --git a/.github/config/add-singularity.yaml b/.github/config/add-containerized.yaml
similarity index 67%
rename from .github/config/add-singularity.yaml
rename to .github/config/add-containerized.yaml
index e8b20d7fad..cc8cd882b4 100644
--- a/.github/config/add-singularity.yaml
+++ b/.github/config/add-containerized.yaml
@@ -3,7 +3,7 @@ description: Bash run in Docker image through Singularity
 default_calc_job_plugin: core.arithmetic.add
 computer: localhost
 filepath_executable: /bin/sh
-image_name: docker://alpine:3
-engine_command: singularity exec --bind $PWD:$PWD {image_name}
+image_name: alpine:3
+engine_command: docker run --user 1001:100 -v $PWD:$PWD -w $PWD -i {image_name}
 prepend_text: ' '
 append_text: ' '
diff --git a/.github/workflows/tests_nightly.sh b/.github/workflows/daemon_tests.sh
similarity index 87%
rename from .github/workflows/tests_nightly.sh
rename to .github/workflows/daemon_tests.sh
index 2712a5124e..8fff830eed 100755
--- a/.github/workflows/tests_nightly.sh
+++ b/.github/workflows/daemon_tests.sh
@@ -12,5 +12,3 @@ verdi -p test_aiida run ${SYSTEM_TESTS}/test_daemon.py
 verdi -p test_aiida run ${SYSTEM_TESTS}/test_containerized_code.py
 bash ${SYSTEM_TESTS}/test_polish_workchains.sh
 verdi daemon stop
-
-AIIDA_TEST_PROFILE=test_aiida pytest --db-backend psql -m nightly tests/
diff --git a/.github/workflows/nightly.yml b/.github/workflows/nightly.yml
index 4f1fc0750f..787793a951 100644
--- a/.github/workflows/nightly.yml
+++ b/.github/workflows/nightly.yml
@@ -27,7 +27,7 @@ jobs:
   nightly-tests:
 
     if: github.repository == 'aiidateam/aiida-core'      # Prevent running the builds on forks as well
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     services:
       postgres:
@@ -55,9 +55,6 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - uses: eWaterCycle/setup-singularity@v7        # for containerized code test
-      with:
-        singularity-version: 3.8.7
 
     - name: Install system dependencies
       run: sudo apt update && sudo apt install postgresql
@@ -72,15 +69,23 @@ jobs:
     - name: Setup environment
       run: .github/workflows/setup.sh
 
-    - name: Run tests
-      id: tests
-      run: .github/workflows/tests_nightly.sh
+    - name: Run pytest nigthly tests
+      id: pytest-tests
+      env:
+        AIIDA_TEST_PROFILE: test_aiida
+        AIIDA_WARN_v3: 1
+      run: |
+        pytest --db-backend psql -m nightly tests/
+
+    - name: Run daemon nightly tests
+      id: daemon-tests
+      run: .github/workflows/daemon_tests.sh
 
     - name: Slack notification
       # Always run this step (otherwise it would be skipped if any of the previous steps fail) but only if the
       # `install` or `tests` steps failed, and the `SLACK_WEBHOOK` is available. The latter is not the case for
       # pull requests that come from forks. This is a limitation of secrets on GHA
-      if: always() && (steps.install.outcome == 'failure' || steps.tests.outcome == 'failure') && env.SLACK_WEBHOOK != null
+      if: always() && (steps.install.outcome == 'failure' || steps.pytest-tests.outcome == 'failure' || steps.daemon-tests.outcome == 'failure') && env.SLACK_WEBHOOK != null
       uses: rtCamp/action-slack-notify@v2
       env:
         SLACK_WEBHOOK: ${{ secrets.SLACK_WEBHOOK }}
diff --git a/.github/workflows/setup.sh b/.github/workflows/setup.sh
index aaa0228d36..9f2b22f35c 100755
--- a/.github/workflows/setup.sh
+++ b/.github/workflows/setup.sh
@@ -19,7 +19,7 @@ verdi computer configure core.local localhost --config "${CONFIG}/localhost-conf
 verdi computer test localhost
 verdi code create core.code.installed --non-interactive --config "${CONFIG}/doubler.yaml"
 verdi code create core.code.installed --non-interactive --config "${CONFIG}/add.yaml"
-verdi code create core.code.containerized --non-interactive --config "${CONFIG}/add-singularity.yaml"
+verdi code create core.code.containerized --non-interactive --config "${CONFIG}/add-containerized.yaml"
 
 # set up slurm-ssh computer
 verdi computer setup --non-interactive --config "${CONFIG}/slurm-ssh.yaml"