diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index 78932871e..fa6c38ef0 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -32,7 +32,7 @@ jobs:
     runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
     env:
       NXF_ANSI_LOG: false
-      JAVA_HOME: $JAVA_HOME_21_X64
+
     strategy:
       matrix:
         NXF_VER:
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index b0d4c13a4..b4579178b 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -28,7 +28,6 @@ concurrency:
 
 env:
   NXF_ANSI_LOG: false
-  JAVA_HOME: $JAVA_HOME_21_X64
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
 jobs:
@@ -52,7 +51,7 @@ jobs:
     needs: prepare-matrix
     env:
       NXF_ANSI_LOG: false
-      JAVA_HOME: $JAVA_HOME_21_X64
+
     strategy:
       matrix:
         TEMPLATE: ${{ fromJson(needs.prepare-matrix.outputs.all_features) }}
@@ -92,6 +91,12 @@ jobs:
           python -m pip install --upgrade pip
           pip install .
 
+      # Set up JAVA_HOME for Java 21
+      - name: Set Java 21
+        run: |
+          echo "JAVA_HOME=$JAVA_HOME_21_X64" >> $GITHUB_ENV
+          echo "PATH=$JAVA_HOME_21_X64/bin:$PATH" >> $GITHUB_ENV
+
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
         with:
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index f69449dde..4ad4d98e0 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -33,7 +33,7 @@ jobs:
     runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
     env:
       NXF_ANSI_LOG: false
-      JAVA_HOME: $JAVA_HOME_21_X64
+
     strategy:
       matrix:
         NXF_VER:
@@ -59,6 +59,12 @@ jobs:
           python -m pip install --upgrade pip
           pip install .
 
+      # Set up JAVA_HOME for Java 21
+      - name: Set Java 21
+        run: |
+          echo "JAVA_HOME=$JAVA_HOME_21_X64" >> $GITHUB_ENV
+          echo "PATH=$JAVA_HOME_21_X64/bin:$PATH" >> $GITHUB_ENV
+
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
         with:
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 76d5d710c..45d08d30b 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -120,6 +120,12 @@ jobs:
         id: date
         run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV
 
+      # Set up JAVA_HOME for Java 21
+      - name: Set Java 21
+        run: |
+          echo "JAVA_HOME=$JAVA_HOME_21_X64" >> $GITHUB_ENV
+          echo "PATH=$JAVA_HOME_21_X64/bin:$PATH" >> $GITHUB_ENV
+
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
diff --git a/nf_core/pipeline-template/.github/workflows/ci.yml b/nf_core/pipeline-template/.github/workflows/ci.yml
index 4f005a1bb..5279d8b6d 100644
--- a/nf_core/pipeline-template/.github/workflows/ci.yml
+++ b/nf_core/pipeline-template/.github/workflows/ci.yml
@@ -11,7 +11,6 @@ on:
 
 env:
   NXF_ANSI_LOG: false
-  JAVA_HOME: $JAVA_HOME_21_X64
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
 
@@ -48,6 +47,12 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
+      # Set up JAVA_HOME for Java 21
+      - name: Set Java 21
+        run: |
+          echo "JAVA_HOME=$JAVA_HOME_21_X64" >> $GITHUB_ENV
+          echo "PATH=$JAVA_HOME_21_X64/bin:$PATH" >> $GITHUB_ENV
+
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
         with:
diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
index 95ebad9fe..4a483f6ed 100644
--- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
+++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
@@ -26,12 +26,17 @@ on:
 
 env:
   NXF_ANSI_LOG: false
-  JAVA_HOME: $JAVA_HOME_21_X64
 
 jobs:
   download:
     runs-on: ubuntu-latest
     steps:
+      # Set up JAVA_HOME for Java 21
+      - name: Set Java 21
+        run: |
+          echo "JAVA_HOME=$JAVA_HOME_21_X64" >> $GITHUB_ENV
+          echo "PATH=$JAVA_HOME_21_X64/bin:$PATH" >> $GITHUB_ENV
+
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
index cfdbcc12a..ede8a3435 100644
--- a/nf_core/pipeline-template/.github/workflows/linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -33,6 +33,12 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
+      # Set up JAVA_HOME for Java 21
+      - name: Set Java 21
+        run: |
+          echo "JAVA_HOME=$JAVA_HOME_21_X64" >> $GITHUB_ENV
+          echo "PATH=$JAVA_HOME_21_X64/bin:$PATH" >> $GITHUB_ENV
+
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2