diff --git a/.github/workflows/scripts/compare_to_generic.sh b/.github/workflows/scripts/compare_to_generic.sh
index 8f046ec9d4..0febce8241 100755
--- a/.github/workflows/scripts/compare_to_generic.sh
+++ b/.github/workflows/scripts/compare_to_generic.sh
@@ -29,16 +29,17 @@ if ! python3 $script_dir/compare_stacks.py $source_of_truth_modules $arch_module
     exit 1
 fi
 
-# Also compare NVIDIA GPU software stacks
-if [[ -n "$CUDA_COMPUTE_CAPABILITIES" ]]; then
-    read -ra compute_capabilities <<< "$CUDA_COMPUTE_CAPABILITIES"
-    echo "Also comparing CUDA-enabled software stacks (for compute capabilities: ${compute_capabilities[@]})"
+# Also compare accelerator software stacks
+if [[ -n "$ACCELERATOR_TARGETS" ]]; then
+    read -ra accel_capabilities <<< "$ACCELERATOR_TARGETS"
+    echo "Also comparing accelerator-enabled software stacks (for compute capabilities: ${accel_capabilities[@]})"
     # Initialize a variable to track failures
     any_failure=0
     # Loop over the array
-    for cc in "${compute_capabilities[@]}"; do
-        source_of_truth_modules="$base_dir/$source_of_truth/accel/nvidia/cc80/$modules_subdir"
-        arch_modules="$base_dir/$target_arch/accel/nvidia/$cc/$modules_subdir"
+    for accel in "${accel_capabilities[@]}"; do
+        source_of_truth_accel="${ACCELERATOR_TARGETS%% *}"  # Just use the first entry as source of truth
+        source_of_truth_modules="$base_dir/$source_of_truth/accel/${source_of_truth_accel}/$modules_subdir"
+        arch_modules="$base_dir/$target_arch/accel/$accel/$modules_subdir"
         echo "Comparing $arch_modules to $source_of_truth_modules"
         if ! python3 $script_dir/compare_stacks.py $source_of_truth_modules $arch_modules; then
             echo "Warning: Comparison failed for compute capability $cc" >&2
@@ -46,9 +47,9 @@ if [[ -n "$CUDA_COMPUTE_CAPABILITIES" ]]; then
         fi
     done
     if [[ $any_failure -ne 0 ]]; then
-        echo "One or more CUDA software stack comparisons failed." >&2
+        echo "One or more accelerator software stack comparisons failed." >&2
         exit 1
     fi
 else
-    echo "CUDA_COMPUTE_CAPABILITIES is not set or is empty, not checking NVIDIA software stacks"
+    echo "ACCELERATOR_TARGETS is not set or is empty, not checking accelerator software stacks"
 fi
diff --git a/.github/workflows/test-software.eessi.io.yml b/.github/workflows/test-software.eessi.io.yml
index e5611e95f3..1f4a087221 100644
--- a/.github/workflows/test-software.eessi.io.yml
+++ b/.github/workflows/test-software.eessi.io.yml
@@ -28,6 +28,7 @@ env:
         - aarch64/neoverse_v1
         - aarch64/nvidia/grace
         - aarch64/a64fx
+
     2025.06:
       x86_64:
         - x86_64/amd/zen2
@@ -46,6 +47,27 @@ env:
         - aarch64/neoverse_v1
         - aarch64/nvidia/grace
         - aarch64/a64fx
+
+    2026.06:
+      x86_64:
+        - x86_64/amd/zen2
+        - x86_64/amd/zen3
+        - x86_64/amd/zen4
+        - x86_64/amd/zen5
+        - x86_64/intel/haswell
+        - x86_64/intel/sapphirerapids
+        - x86_64/intel/skylake_avx512
+        - x86_64/intel/icelake
+        - x86_64/intel/cascadelake
+        - x86_64/generic
+      aarch64:
+        - aarch64/generic
+        - aarch64/neoverse_n1
+        - aarch64/neoverse_v1
+        - aarch64/nvidia/grace
+        - aarch64/a64fx
+        - aarch64/aws/graviton4
+
   # list below should correspond with table @ https://eessi.io/docs/software_layer/gpu_targets/
   EESSI_ACCELERATOR_TARGETS: |
     2023.06:
@@ -60,8 +82,8 @@ env:
         - nvidia/cc80
         - nvidia/cc90
       aarch64/a64fx: []
+
     2025.06:
-      # Provide a default set of compute capabilities
       default:
         - nvidia/cc70
         - nvidia/cc80
@@ -76,7 +98,47 @@ env:
         - amd/gfx1101
         - amd/gfx1200
         - amd/gfx1201
-      # and then allow for special cases for specific architectures
+      aarch64/generic:
+        - nvidia/cc70
+        - nvidia/cc80
+        - nvidia/cc90
+        - nvidia/cc100
+        - nvidia/cc120
+      aarch64/neoverse_n1:
+        - nvidia/cc70
+        - nvidia/cc80
+        - nvidia/cc90
+        - nvidia/cc100
+        - nvidia/cc120
+      aarch64/neoverse_v1:
+        - nvidia/cc70
+        - nvidia/cc80
+        - nvidia/cc90
+        - nvidia/cc100
+        - nvidia/cc120
+      aarch64/nvidia/grace:
+        - nvidia/cc70
+        - nvidia/cc80
+        - nvidia/cc90
+        - nvidia/cc100
+        - nvidia/cc120
+      aarch64/a64fx: []
+
+    2026.06:
+      default:
+        - nvidia/cc70
+        - nvidia/cc80
+        - nvidia/cc90
+        - nvidia/cc100
+        - nvidia/cc120
+        - amd/gfx908
+        - amd/gfx90a
+        - amd/gfx942
+        - amd/gfx1030
+        - amd/gfx1100
+        - amd/gfx1101
+        - amd/gfx1200
+        - amd/gfx1201
       aarch64/generic:
         - nvidia/cc70
         - nvidia/cc80
@@ -148,6 +210,7 @@ jobs:
           echo "EOF" >> "$GITHUB_OUTPUT"
           
   requires_forced_ci:
+    if: github.event_name == 'pull_request'
     runs-on: ubuntu-24.04
     needs: check_EESSI_version_changed_files
     steps:
@@ -180,15 +243,21 @@ jobs:
           # Arm CPU targets (EESSI 2023.06)
           - runs_on: ubuntu-24.04-arm
             EESSI_VERSION: 2023.06
-          # Arm CPU targets (EESSI 2025.06)
-          - runs_on: ubuntu-24.04-arm
-            EESSI_VERSION: 2025.06
           # x86_64 CPU targets (EESSI 2023.06)
           - runs_on: ubuntu-24.04
             EESSI_VERSION: 2023.06
+          # Arm CPU targets (EESSI 2025.06)
+          - runs_on: ubuntu-24.04-arm
+            EESSI_VERSION: 2025.06
           # x86_64 CPU targets (EESSI 2025.06)
           - runs_on: ubuntu-24.04
             EESSI_VERSION: 2025.06
+          # Arm CPU targets (EESSI 2026.06)
+          - runs_on: ubuntu-24.04-arm
+            EESSI_VERSION: 2026.06
+          # x86_64 CPU targets (EESSI 2026.06)
+          - runs_on: ubuntu-24.04
+            EESSI_VERSION: 2026.06
 
     runs-on: ${{ matrix.runs_on }}
     steps:
@@ -209,12 +278,10 @@ jobs:
           echo "lscpu:"
           lscpu
 
-      - name: Mount EESSI CernVM-FS pilot repository
-        uses: cvmfs-contrib/github-action-cvmfs@10197e000cc0add8e54ac4fb73d3ed44e2de72b4 # v5.5
+      - name: Mount EESSI CernVM-FS repository
+        uses: eessi/github-action-eessi@v3
         with:
-          cvmfs_config_package: https://github.com/EESSI/filesystem-layer/releases/download/latest/cvmfs-config-eessi_latest_all.deb
-          cvmfs_http_proxy: DIRECT
-          cvmfs_repositories: software.eessi.io
+          eessi_stack_version: '${{matrix.EESSI_VERSION}}'
 
       - name: Check for missing installations
         if: >
@@ -224,9 +291,6 @@ jobs:
             matrix.EESSI_VERSION
           )
         run: |
-          # Do a basic initialisation to set up Lmod and EESSI modules
-          export EESSI_MODULE_STICKY=1
-          source /cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}/init/lmod/bash
 
           # From this extract the CPUs we need to loop over
           cpu_subdirs=$(echo "${EESSI_CPU_TARGETS}" | yq ".\"${EESSI_VERSION}\".\"${EESSI_CPU_FAMILY}\" | .[]")
@@ -254,7 +318,7 @@ jobs:
                 
 
               (
-                set -euo pipefail
+                set -e -o pipefail
 
                 module --force purge
                 export EESSI_SOFTWARE_SUBDIR_OVERRIDE="$cpu"
diff --git a/.github/workflows/test_compare_stacks.yml b/.github/workflows/test_compare_stacks.yml
index 4e3a8db6f6..03a7a65679 100644
--- a/.github/workflows/test_compare_stacks.yml
+++ b/.github/workflows/test_compare_stacks.yml
@@ -1,89 +1,260 @@
-# documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
 name: Check for discrepancies between software stacks in software.eessi.io
+
 on:
-  push:
-    branches: [ "main" ]
-  pull_request:
+  workflow_run:
+    workflows:
+      - Check for missing software installations in software.eessi.io
+    types:
+      - completed
+
   workflow_dispatch:
+
 permissions:
-  contents: read # to fetch code (actions/checkout)
+  contents: read
+
 env:
-  CUDA_COMPUTE_CAPABILITIES_YAML: |
+  # list below should correspond with table @ https://eessi.io/docs/software_layer/cpu_targets/
+  EESSI_CPU_TARGETS: |
+    2023.06:
+      x86_64:
+        - x86_64/amd/zen2
+        - x86_64/amd/zen3
+        - x86_64/amd/zen4
+        - x86_64/intel/haswell
+        - x86_64/intel/sapphirerapids
+        - x86_64/intel/skylake_avx512
+        - x86_64/intel/icelake
+        - x86_64/intel/cascadelake
+        - x86_64/generic
+      aarch64:
+        - aarch64/generic
+        - aarch64/neoverse_n1
+        - aarch64/neoverse_v1
+        - aarch64/nvidia/grace
+        - aarch64/a64fx
+
+    2025.06:
+      x86_64:
+        - x86_64/amd/zen2
+        - x86_64/amd/zen3
+        - x86_64/amd/zen4
+        - x86_64/amd/zen5
+        - x86_64/intel/haswell
+        - x86_64/intel/sapphirerapids
+        - x86_64/intel/skylake_avx512
+        - x86_64/intel/icelake
+        - x86_64/intel/cascadelake
+        - x86_64/generic
+      aarch64:
+        - aarch64/generic
+        - aarch64/neoverse_n1
+        - aarch64/neoverse_v1
+        - aarch64/nvidia/grace
+        - aarch64/a64fx
+
+    2026.06:
+      x86_64:
+        - x86_64/amd/zen2
+        - x86_64/amd/zen3
+        - x86_64/amd/zen4
+        - x86_64/amd/zen5
+        - x86_64/intel/haswell
+        - x86_64/intel/sapphirerapids
+        - x86_64/intel/skylake_avx512
+        - x86_64/intel/icelake
+        - x86_64/intel/cascadelake
+        - x86_64/generic
+      aarch64:
+        - aarch64/generic
+        - aarch64/neoverse_n1
+        - aarch64/neoverse_v1
+        - aarch64/nvidia/grace
+        - aarch64/a64fx
+        - aarch64/aws/graviton4
+
+  # list below should correspond with table @ https://eessi.io/docs/software_layer/gpu_targets/
+  EESSI_ACCELERATOR_TARGETS: |
     2023.06:
       # Provide a default set of compute capabilities
       default:
-        - cc70
-        - cc80
-        - cc90
+        - nvidia/cc70
+        - nvidia/cc80
+        - nvidia/cc90
       # and then allow for special cases for specific architectures
       x86_64/amd/zen2:
-        - cc70
-        - cc80
-        - cc90
+        - nvidia/cc70
+        - nvidia/cc80
+        - nvidia/cc90
       aarch64/a64fx: []
+
     2025.06:
-      # Provide a default set of compute capabilities
       default:
-        - cc70
-        - cc80
-        - cc90
-        - cc100
-        - cc120
+        - nvidia/cc70
+        - nvidia/cc80
+        - nvidia/cc90
+        - nvidia/cc100
+        - nvidia/cc120
+        - amd/gfx908
+        - amd/gfx90a
+        - amd/gfx942
+        - amd/gfx1030
+        - amd/gfx1100
+        - amd/gfx1101
+        - amd/gfx1200
+        - amd/gfx1201
+      aarch64/generic:
+        - nvidia/cc70
+        - nvidia/cc80
+        - nvidia/cc90
+        - nvidia/cc100
+        - nvidia/cc120
+      aarch64/neoverse_n1:
+        - nvidia/cc70
+        - nvidia/cc80
+        - nvidia/cc90
+        - nvidia/cc100
+        - nvidia/cc120
+      aarch64/neoverse_v1:
+        - nvidia/cc70
+        - nvidia/cc80
+        - nvidia/cc90
+        - nvidia/cc100
+        - nvidia/cc120
+      aarch64/nvidia/grace:
+        - nvidia/cc70
+        - nvidia/cc80
+        - nvidia/cc90
+        - nvidia/cc100
+        - nvidia/cc120
+      aarch64/a64fx: []
+
+    2026.06:
+      default:
+        - nvidia/cc70
+        - nvidia/cc80
+        - nvidia/cc90
+        - nvidia/cc100
+        - nvidia/cc120
+        - amd/gfx908
+        - amd/gfx90a
+        - amd/gfx942
+        - amd/gfx1030
+        - amd/gfx1100
+        - amd/gfx1101
+        - amd/gfx1200
+        - amd/gfx1201
+      aarch64/generic:
+        - nvidia/cc70
+        - nvidia/cc80
+        - nvidia/cc90
+        - nvidia/cc100
+        - nvidia/cc120
+      aarch64/neoverse_n1:
+        - nvidia/cc70
+        - nvidia/cc80
+        - nvidia/cc90
+        - nvidia/cc100
+        - nvidia/cc120
+      aarch64/neoverse_v1:
+        - nvidia/cc70
+        - nvidia/cc80
+        - nvidia/cc90
+        - nvidia/cc100
+        - nvidia/cc120
+      aarch64/nvidia/grace:
+        - nvidia/cc70
+        - nvidia/cc80
+        - nvidia/cc90
+        - nvidia/cc100
+        - nvidia/cc120
       aarch64/a64fx: []
 jobs:
   compare_stacks:
-    runs-on: ubuntu-24.04
+    # Only run after the missing-installation workflow succeeds.
+    # workflow_run itself is triggered for every completed run, but this
+    # prevents this job from running for failed/cancelled upstream runs.
+    if: >
+      github.event_name == 'workflow_dispatch'
+      || github.event.workflow_run.conclusion == 'success'
+
     strategy:
       fail-fast: false
       matrix:
-        EESSI_VERSION:
-          - 2023.06
-          - 2025.06
-          - 2026.06
-        COMPARISON_ARCH:
-          - aarch64/a64fx
-          - aarch64/aws/graviton4
-          - aarch64/neoverse_n1
-          - aarch64/neoverse_v1
-          - aarch64/nvidia/grace
-          - x86_64/amd/zen2
-          - x86_64/amd/zen3
-          - x86_64/amd/zen4
-          - x86_64/amd/zen5
-          - x86_64/intel/haswell
-          - x86_64/intel/skylake_avx512
-          - x86_64/intel/sapphirerapids
-          - x86_64/intel/icelake
-          - x86_64/intel/cascadelake
-        exclude:
-          # amd/zen5 only supported since EESSI 2025.06
-          - EESSI_VERSION: 2023.06
-            COMPARISON_ARCH: x86_64/amd/zen5
-          # aws/graviton4 only supported since EESSI 2026.06
-          - EESSI_VERSION: 2023.06
-            COMPARISON_ARCH: aarch64/aws/graviton4
-          - EESSI_VERSION: 2025.06
-            COMPARISON_ARCH: aarch64/aws/graviton4
+        include:
+          # Arm CPU targets (EESSI 2023.06)
+          - runs_on: ubuntu-24.04-arm
+            EESSI_VERSION: 2023.06
+          # x86_64 CPU targets (EESSI 2023.06)
+          - runs_on: ubuntu-24.04
+            EESSI_VERSION: 2023.06
+          # Arm CPU targets (EESSI 2025.06)
+          - runs_on: ubuntu-24.04-arm
+            EESSI_VERSION: 2025.06
+          # x86_64 CPU targets (EESSI 2025.06)
+          - runs_on: ubuntu-24.04
+            EESSI_VERSION: 2025.06
+            # Arm CPU targets (EESSI 2026.06)
+          - runs_on: ubuntu-24.04-arm
+            EESSI_VERSION: 2026.06
+          # x86_64 CPU targets (EESSI 2026.06)
+          - runs_on: ubuntu-24.04
+            EESSI_VERSION: 2026.06
+
+    runs-on: ${{ matrix.runs_on }}
+
     steps:
-        - name: Check out software-layer repository
-          uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
-
-        - name: Mount EESSI CernVM-FS pilot repository
-          uses: eessi/github-action-eessi@v3
-
-        - name: Compare stacks
-          run: |
-              export EESSI_PREFIX=/cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}
-              export EESSI_OS_TYPE=linux
-              env | grep ^EESSI | sort
-
-              # Compare the requested architecture to the generic stack
-              # (assumes the general structure /cvmfs/software.eessi.io/versions/2023.06/software/linux/$COMPARISON_ARCH/modules/all)
-              # and include a check for CUDA-enabled software using the environment variable CUDA_COMPUTE_CAPABILITIES
-              # (which assumes the structure /cvmfs/software.eessi.io/versions/2023.06/software/linux/$COMPARISON_ARCH/accel/nvidia/$cc/modules/all)
-              
-              # Parse the yaml that makes the compute capabilities arch-dependent
-              CUDA_COMPUTE_CAPABILITIES=$(echo "${CUDA_COMPUTE_CAPABILITIES_YAML}" | yq ".\"${{matrix.EESSI_VERSION}}\".\"${{matrix.COMPARISON_ARCH}}\" // .\"${{matrix.EESSI_VERSION}}\".default | .[]" | tr '\n' ' ')
-              export CUDA_COMPUTE_CAPABILITIES=${CUDA_COMPUTE_CAPABILITIES%% }  # trim trailing space
-              
-              .github/workflows/scripts/compare_to_generic.sh ${EESSI_PREFIX}/software/${EESSI_OS_TYPE} ${{matrix.COMPARISON_ARCH}}
+      - name: Check out software-layer repository
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          # For workflow_run events, check the exact commit that was tested
+          # by the upstream workflow.
+          ref: ${{ github.event_name == 'workflow_run' && github.event.workflow_run.head_sha || github.sha }}
+
+      - name: Mount EESSI CernVM-FS repository
+        uses: eessi/github-action-eessi@v3
+        with:
+          eessi_stack_version: '${{matrix.EESSI_VERSION}}'        
+
+      - name: Compare stacks
+        shell: bash
+        run: |
+          echo "::group::EESSI ${EESSI_VERSION} / ${EESSI_CPU_FAMILY}"
+
+          # Get all CPU targets belonging to this architecture family.
+          CPU_TARGETS=$(echo "${EESSI_CPU_TARGETS}" \
+            | yq -r ".\"${EESSI_VERSION}\".\"${EESSI_CPU_FAMILY}\"[]")
+
+          for COMPARISON_ARCH in ${CPU_TARGETS}; do
+            echo "::group::Compare ${EESSI_VERSION} / ${COMPARISON_ARCH}"
+
+            # Use architecture-specific accelerator targets where defined,
+            # otherwise fall back to the default set.
+            ALL_ACCELERATOR_TARGETS=$(echo "${EESSI_ACCELERATOR_TARGETS}" \
+              | yq ".\"${{ matrix.EESSI_VERSION }}\".\"${COMPARISON_ARCH}\" // .\"${{ matrix.EESSI_VERSION }}\".default | .[]" \
+              | tr '\n' ' ')
+
+            echo "COMPARISON_ARCH=${COMPARISON_ARCH}"
+            echo "ACCELERATOR_TARGETS=${ALL_ACCELERATOR_TARGETS}"
+
+            for ACCELERATOR_TYPE in nvidia amd; do
+              ACCELERATOR_TARGETS_TYPE=$(echo "${ALL_ACCELERATOR_TARGETS}" \
+                | tr ' ' '\n' \
+                | grep "^${ACCELERATOR_TYPE}/" \
+                | tr '\n' ' ' || true)
+
+              if [[ -z "${ACCELERATOR_TARGETS_TYPE}" ]]; then
+                continue
+              fi
+
+              export ACCELERATOR_TARGETS="${ACCELERATOR_TARGETS_TYPE}"
+
+              echo "Comparing ${ACCELERATOR_TYPE} accelerator targets:"
+              echo "ACCELERATOR_TARGETS=${ACCELERATOR_TARGETS}"
+
+              .github/workflows/scripts/compare_to_generic.sh \
+                "${EESSI_PREFIX}/software/${EESSI_OS_TYPE}" \
+                "${COMPARISON_ARCH}"
+            done
+
+            echo "::endgroup::"
+          done