diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index b4579178bd..78d174434b 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -91,11 +91,10 @@ 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
+      - uses: actions/setup-java@v4
+        with:
+          java-version: "21"
+          distribution: "temurin"
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 4ad4d98e0d..55b64f9cfb 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -59,11 +59,10 @@ 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
+      - uses: actions/setup-java@v4
+        with:
+          java-version: "21"
+          distribution: "temurin"
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 45d08d30ba..dcf5f0b0cc 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -120,11 +120,10 @@ 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
+      - uses: actions/setup-java@v4
+        with:
+          java-version: "21"
+          distribution: "temurin"
 
       - 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 5279d8b6d6..d022850ec5 100644
--- a/nf_core/pipeline-template/.github/workflows/ci.yml
+++ b/nf_core/pipeline-template/.github/workflows/ci.yml
@@ -47,11 +47,10 @@ 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
+      - uses: actions/setup-java@v4
+        with:
+          java-version: "21"
+          distribution: "temurin"
 
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
index 4a483f6ed6..5d483bd0a4 100644
--- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
+++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
@@ -31,11 +31,10 @@ 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
+      - uses: actions/setup-java@v4
+        with:
+          java-version: "21"
+          distribution: "temurin"
 
       - 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 ede8a34355..a6150781c3 100644
--- a/nf_core/pipeline-template/.github/workflows/linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -33,11 +33,10 @@ 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
+      - uses: actions/setup-java@v4
+        with:
+          java-version: "21"
+          distribution: "temurin"
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2