diff --git a/end-to-end-tests.yml b/end-to-end-tests.yml
index 3c8ab0780..f18a5151f 100644
--- a/end-to-end-tests.yml
+++ b/end-to-end-tests.yml
@@ -23,6 +23,10 @@ jobs:
     inputs:
       versionSpec: '3.12'
       addToPath: true
+  - bash: |
+      mkdir -p ~/.pyrit
+    displayName: "Create PyRIT configuration directory"
+    name: create_pyrit_dir
   - task: AzureKeyVault@2
     displayName: Azure Key Vault - retrieve .env file secret
     inputs:
@@ -36,13 +40,13 @@ jobs:
       secret = os.environ.get('PYRIT_TEST_SECRET');
       if not secret:
         raise ValueError('PYRIT_TEST_SECRET is not set');
-      with open('.env', 'w') as file:
+      with open(os.path.expanduser('~/.pyrit/.env'), 'w') as file:
         file.write(secret)"
     env:
       PYRIT_TEST_SECRET: $(env-global)
     name: create_env_file
   - bash: |
-      cp build_scripts/env_local_integration_test .env.local
+      cp build_scripts/env_local_integration_test ~/.pyrit/.env.local
     displayName: "Create .env.local from example"
   - script:
       wget -qO- https://astral.sh/uv/install.sh | sh
@@ -83,8 +87,6 @@ jobs:
       NEW_DIR="e2e_test_directory"
       cd ..
       mkdir -p $NEW_DIR/tests
-      cp $PyRIT_DIR/.env $NEW_DIR
-      cp $PyRIT_DIR/.env.local $NEW_DIR
       cp -r $PyRIT_DIR/doc $NEW_DIR
       cp -r $PyRIT_DIR/assets $NEW_DIR
       cp -r $PyRIT_DIR/tests/end_to_end $NEW_DIR/tests
@@ -112,7 +114,7 @@ jobs:
         # Run end-to-end tests
         make end-to-end-test
   - bash: |
-      rm -f .env
+      rm -f ~/.pyrit/.env ~/.pyrit/.env.local
     name: clean_up_env_files
     condition: always()
   - task: PublishTestResults@2
diff --git a/integration-tests.yml b/integration-tests.yml
index 9b54218f7..ff6fe4d0e 100644
--- a/integration-tests.yml
+++ b/integration-tests.yml
@@ -21,6 +21,10 @@ jobs:
     inputs:
       versionSpec: '3.12'
       addToPath: true
+  - bash: |
+      mkdir -p ~/.pyrit
+    displayName: "Create PyRIT configuration directory"
+    name: create_pyrit_dir
   - task: AzureKeyVault@2
     displayName: Azure Key Vault - retrieve .env file secret
     inputs:
@@ -34,13 +38,13 @@ jobs:
       secret = os.environ.get('PYRIT_TEST_SECRET');
       if not secret:
         raise ValueError('PYRIT_TEST_SECRET is not set');
-      with open('.env', 'w') as file:
+      with open(os.path.expanduser('~/.pyrit/.env'), 'w') as file:
         file.write(secret)"
     env:
       PYRIT_TEST_SECRET: $(env-global)
     name: create_env_file
   - bash: |
-      cp build_scripts/env_local_integration_test .env.local
+      cp build_scripts/env_local_integration_test ~/.pyrit/.env.local
     displayName: "Create .env.local from example"
   - script:
       wget -qO- https://astral.sh/uv/install.sh | sh
@@ -81,8 +85,6 @@ jobs:
       NEW_DIR="integration_test_directory"
       cd ..
       mkdir -p $NEW_DIR/tests
-      cp $PyRIT_DIR/.env $NEW_DIR
-      cp $PyRIT_DIR/.env.local $NEW_DIR
       cp -r $PyRIT_DIR/doc $NEW_DIR
       cp -r $PyRIT_DIR/assets $NEW_DIR
       cp -r $PyRIT_DIR/tests/integration $NEW_DIR/tests
@@ -110,7 +112,7 @@ jobs:
         # Run integration tests
         make integration-test
   - bash: |
-      rm -f .env
+      rm -f ~/.pyrit/.env ~/.pyrit/.env.local
     name: clean_up_env_files
     condition: always()
   - task: PublishTestResults@2