diff --git a/src/src/LocalTests/ConfigurationProcessor.php b/src/src/LocalTests/ConfigurationProcessor.php
index 45d2a83d..068b941d 100644
--- a/src/src/LocalTests/ConfigurationProcessor.php
+++ b/src/src/LocalTests/ConfigurationProcessor.php
@@ -93,11 +93,8 @@ public function process_configuration(
 			$this->normalize_plugins( $env_config );
 			$this->normalize_themes( $env_config );
 
-			if ( $sut_type === 'theme' ) {
-				$env_up_options['--theme'] = array_values( $env_config['themes'] );
-			} else {
-				$env_up_options['--plugin'] = array_values( $env_config['plugins'] );
-			}
+			$env_up_options['--plugin'] = array_values( $env_config['plugins'] );
+			$env_up_options['--theme']  = array_values( $env_config['themes'] );
 		}
 
 		if ( App::getVar( 'QIT_ACTIVATION_TEST' ) ) {
@@ -160,11 +157,8 @@ protected function finalize_sut_definition(
 			$this->add_cli_plugins( $env_config, $input );
 			$this->normalize_plugins( $env_config );
 			$this->normalize_themes( $env_config );
-			if ( $sut_type === 'theme' ) {
-				$env_up_options['--theme'] = array_values( $env_config['themes'] );
-			} else {
-				$env_up_options['--plugin'] = array_values( $env_config['plugins'] );
-			}
+			$env_up_options['--plugin'] = array_values( $env_config['plugins'] );
+			$env_up_options['--theme']  = array_values( $env_config['themes'] );
 
 			return;
 		}
@@ -213,11 +207,8 @@ protected function finalize_sut_definition(
 		$this->normalize_plugins( $env_config );
 		$this->normalize_themes( $env_config );
 
-		if ( $sut_type === 'theme' ) {
-			$env_up_options['--theme'] = array_values( $env_config['themes'] );
-		} else {
-			$env_up_options['--plugin'] = array_values( $env_config['plugins'] );
-		}
+		$env_up_options['--theme'] = array_values( $env_config['themes'] );
+		$env_up_options['--plugin'] = array_values( $env_config['plugins'] );
 	}
 
 	/**
diff --git a/src/tests/Environment/RunActivationCommandTest.php b/src/tests/Environment/RunActivationCommandTest.php
index 307dd641..2d4c022d 100644
--- a/src/tests/Environment/RunActivationCommandTest.php
+++ b/src/tests/Environment/RunActivationCommandTest.php
@@ -314,6 +314,22 @@ public function test_activation_with_additional_plugins() {
 		$this->assertMatchesJsonSnapshot( $this->application_tester->getDisplay() );
 	}
 
+	public function test_theme_sut_activation() {
+		putenv( 'QIT_TESTING_ENV_CONFIG=1' );
+
+		$fixture_dir = $this->scenarios_dir . 'scenario-theme-activation';
+		$this->assertDirectoryExists( $fixture_dir );
+		chdir( $fixture_dir );
+
+		$this->application_tester->run( [
+			'command'       => 'run:activation',
+			'woo_extension' => 'storefront', // This is a known theme slug from your mock.
+		], [ 'capture_stderr_separately' => true ] );
+
+		$this->assertCommandIsSuccessful( $this->application_tester );
+		$this->assertMatchesJsonSnapshot( $this->application_tester->getDisplay() );
+	}
+
 	public function tearDown(): void {
 		parent::tearDown();
 		putenv( 'QIT_TESTING_ENV_CONFIG' );
diff --git a/src/tests/Environment/RunE2ECommandTest.php b/src/tests/Environment/RunE2ECommandTest.php
index cb6e7d76..6fd4f52a 100644
--- a/src/tests/Environment/RunE2ECommandTest.php
+++ b/src/tests/Environment/RunE2ECommandTest.php
@@ -820,6 +820,20 @@ public function test_numeric_plugin_id_with_qit_config() {
 		$this->assertMatchesJsonSnapshot($output);
 	}
 
+	public function test_theme_sut_with_additional_plugins() {
+		putenv( 'QIT_TESTING_ENV_CONFIG=1' );
 
+		$fixture_dir = $this->scenarios_dir . 'scenario-theme-sut';
+		$this->assertDirectoryExists( $fixture_dir );
+		chdir( $fixture_dir );
+
+		$this->application_tester->run( [
+			'command'       => 'run:e2e',
+			'woo_extension' => 'storefront', // a theme SUT
+			'--plugin'      => [ 'woocommerce:test:activation' ], // triggers previous issue
+		], [ 'capture_stderr_separately' => true ] );
 
+		$this->assertCommandIsSuccessful( $this->application_tester );
+		$this->assertMatchesJsonSnapshot( $this->application_tester->getDisplay() );
+	}
 }
diff --git a/src/tests/Environment/__snapshots__/RunActivationCommandTest__test_theme_sut_activation__1.json b/src/tests/Environment/__snapshots__/RunActivationCommandTest__test_theme_sut_activation__1.json
new file mode 100644
index 00000000..183ebe4f
--- /dev/null
+++ b/src/tests/Environment/__snapshots__/RunActivationCommandTest__test_theme_sut_activation__1.json
@@ -0,0 +1,33 @@
+{
+    "--php_version": "7.4",
+    "--wp": "stable",
+    "--plugin": [
+        {
+            "slug": "woocommerce",
+            "source": "woocommerce",
+            "test_tags": [
+                "activation"
+            ],
+            "action": "test"
+        }
+    ],
+    "--theme": [
+        {
+            "source": ".\/storefront-theme",
+            "test_tags": [
+                "pre-activation"
+            ],
+            "action": "bootstrap",
+            "slug": "storefront"
+        }
+    ],
+    "--volume": [],
+    "--php_extension": [],
+    "--require": [],
+    "--object_cache": false,
+    "--skip_activating_plugins": true,
+    "--tunnel": "no_tunnel",
+    "--json": true,
+    "--env": [],
+    "--env_file": []
+}
diff --git a/src/tests/Environment/__snapshots__/RunE2ECommandTest__test_plugin_and_theme_sut_theme__1.json b/src/tests/Environment/__snapshots__/RunE2ECommandTest__test_plugin_and_theme_sut_theme__1.json
index adbbc996..504b5b59 100644
--- a/src/tests/Environment/__snapshots__/RunE2ECommandTest__test_plugin_and_theme_sut_theme__1.json
+++ b/src/tests/Environment/__snapshots__/RunE2ECommandTest__test_plugin_and_theme_sut_theme__1.json
@@ -1,7 +1,16 @@
 {
     "--php_version": "7.4",
     "--wp": "stable",
-    "--plugin": [],
+    "--plugin": [
+        {
+            "source": ".\/woocommerce-sample-plugin",
+            "test_tags": [
+                "default"
+            ],
+            "action": "bootstrap",
+            "slug": "woocommerce-sample-plugin"
+        }
+    ],
     "--theme": [
         {
             "source": ".\/deli-theme",
diff --git a/src/tests/Environment/__snapshots__/RunE2ECommandTest__test_theme_and_plugin_both_config__1.json b/src/tests/Environment/__snapshots__/RunE2ECommandTest__test_theme_and_plugin_both_config__1.json
index 21854d28..dc43b33f 100644
--- a/src/tests/Environment/__snapshots__/RunE2ECommandTest__test_theme_and_plugin_both_config__1.json
+++ b/src/tests/Environment/__snapshots__/RunE2ECommandTest__test_theme_and_plugin_both_config__1.json
@@ -1,7 +1,16 @@
 {
     "--php_version": "7.4",
     "--wp": "stable",
-    "--plugin": [],
+    "--plugin": [
+        {
+            "source": ".\/woocommerce-sample-plugin",
+            "test_tags": [
+                "default"
+            ],
+            "action": "bootstrap",
+            "slug": "woocommerce-sample-plugin"
+        }
+    ],
     "--theme": [
         {
             "source": ".\/twentytwentyone-theme",
diff --git a/src/tests/Environment/__snapshots__/RunE2ECommandTest__test_theme_sut_with_additional_plugins__1.json b/src/tests/Environment/__snapshots__/RunE2ECommandTest__test_theme_sut_with_additional_plugins__1.json
new file mode 100644
index 00000000..6cc23a88
--- /dev/null
+++ b/src/tests/Environment/__snapshots__/RunE2ECommandTest__test_theme_sut_with_additional_plugins__1.json
@@ -0,0 +1,33 @@
+{
+    "--php_version": "7.4",
+    "--wp": "stable",
+    "--plugin": [
+        {
+            "slug": "woocommerce",
+            "source": "woocommerce",
+            "test_tags": [
+                "activation"
+            ],
+            "action": "test"
+        }
+    ],
+    "--theme": [
+        {
+            "source": ".\/storefront-theme",
+            "test_tags": [
+                "default"
+            ],
+            "action": "test",
+            "slug": "storefront"
+        }
+    ],
+    "--volume": [],
+    "--php_extension": [],
+    "--require": [],
+    "--object_cache": false,
+    "--skip_activating_plugins": false,
+    "--tunnel": "no_tunnel",
+    "--json": true,
+    "--env": [],
+    "--env_file": []
+}
diff --git a/src/tests/Environment/__snapshots__/RunE2ECommandTest__test_theme_with_additional_plugin__1.json b/src/tests/Environment/__snapshots__/RunE2ECommandTest__test_theme_with_additional_plugin__1.json
index 8e813a8c..5946da0d 100644
--- a/src/tests/Environment/__snapshots__/RunE2ECommandTest__test_theme_with_additional_plugin__1.json
+++ b/src/tests/Environment/__snapshots__/RunE2ECommandTest__test_theme_with_additional_plugin__1.json
@@ -2,7 +2,14 @@
     "--php_version": "7.4",
     "--wp": "stable",
     "--plugin": [
-        "woocommerce-extra-plugin:bootstrap"
+        {
+            "slug": "woocommerce-extra-plugin",
+            "source": "woocommerce-extra-plugin",
+            "test_tags": [
+                "default"
+            ],
+            "action": "bootstrap"
+        }
     ],
     "--theme": [
         {
diff --git a/src/tests/data/rune2e-scenarios/scenario-theme-activation/qit.yml b/src/tests/data/rune2e-scenarios/scenario-theme-activation/qit.yml
new file mode 100644
index 00000000..2777ac62
--- /dev/null
+++ b/src/tests/data/rune2e-scenarios/scenario-theme-activation/qit.yml
@@ -0,0 +1,5 @@
+themes:
+  storefront:
+    source: "./storefront-theme"
+    test_tags:
+      - "default"
\ No newline at end of file
diff --git a/src/tests/data/rune2e-scenarios/scenario-theme-activation/storefront-theme/style.css b/src/tests/data/rune2e-scenarios/scenario-theme-activation/storefront-theme/style.css
new file mode 100644
index 00000000..361ea929
--- /dev/null
+++ b/src/tests/data/rune2e-scenarios/scenario-theme-activation/storefront-theme/style.css
@@ -0,0 +1,6 @@
+/*
+Theme Name: Storefront
+Author: Automattic
+Description: The perfect theme for your next WooCommerce project.
+Version: 2.5.0
+*/
\ No newline at end of file
diff --git a/src/tests/data/rune2e-scenarios/scenario-theme-activation/tests/example.spec.js b/src/tests/data/rune2e-scenarios/scenario-theme-activation/tests/example.spec.js
new file mode 100644
index 00000000..13f888bc
--- /dev/null
+++ b/src/tests/data/rune2e-scenarios/scenario-theme-activation/tests/example.spec.js
@@ -0,0 +1,6 @@
+import { test, expect } from '@playwright/test';
+
+test('Storefront theme activation test', async ({ page }) => {
+    // Placeholder test
+    expect(1).toBe(1);
+});
\ No newline at end of file