diff --git a/gradle-plugin/src/main/java/com/microsoft/gradle/GradleProjectModelBuilder.java b/gradle-plugin/src/main/java/com/microsoft/gradle/GradleProjectModelBuilder.java
index 6b8bcd4e0..065dbc904 100644
--- a/gradle-plugin/src/main/java/com/microsoft/gradle/GradleProjectModelBuilder.java
+++ b/gradle-plugin/src/main/java/com/microsoft/gradle/GradleProjectModelBuilder.java
@@ -103,19 +103,9 @@ private GradleProjectModel buildModel(Project project, String rootProjectName, D
 		GradleDependencyNode node = generateDefaultGradleDependencyNode(project);
 		List<String> plugins = getPlugins(project);
 		List<GradleClosure> closures = getPluginClosures(project);
+		// For isolated projects, sub-models will be built separately via individual buildAll calls
+		// Each project model is built in isolation, avoiding cross-project access
 		List<GradleProjectModel> subModels = new ArrayList<>();
-		for (DefaultGradleProject subDefaultGradleProject : gradleProject.getChildren()) {
-			// Query sub projects when both gradleProject and project contain them
-			Map<String, Project> childProjects = project.getChildProjects();
-			String projectName = subDefaultGradleProject.getName();
-			if (childProjects.keySet().contains(projectName)) {
-				GradleProjectModel subModel = buildModel(childProjects.get(projectName), rootProjectName,
-						subDefaultGradleProject);
-				if (subModel != null) {
-					subModels.add(subModel);
-				}
-			}
-		}
 		List<GradleTask> tasks = getGradleTasks(project, rootProjectName, gradleProject);
 		return new DefaultGradleProjectModel(project.getParent() == null, project.getProjectDir().getAbsolutePath(),
 				subModels, tasks, node, plugins, closures, scriptClasspaths);
diff --git a/gradle-server/src/main/java/com/github/badsyntax/gradle/utils/PluginUtils.java b/gradle-server/src/main/java/com/github/badsyntax/gradle/utils/PluginUtils.java
index 9b74c6aa4..0f43b2a04 100644
--- a/gradle-server/src/main/java/com/github/badsyntax/gradle/utils/PluginUtils.java
+++ b/gradle-server/src/main/java/com/github/badsyntax/gradle/utils/PluginUtils.java
@@ -31,8 +31,8 @@ public static File getInitScript() {
 			// handle init script
 			String pluginJarUnixPath = pluginJarFile.getAbsolutePath().replace("\\", "/");
 			String initScriptContent = "initscript {\n" + "	dependencies {\n" + "		classpath files('"
-					+ pluginJarUnixPath + "')\n" + "	}\n" + "}\n" + "\n" + "allprojects {\n"
-					+ "	apply plugin: com.microsoft.gradle.GradlePlugin\n" + "}\n";
+					+ pluginJarUnixPath + "')\n" + "	}\n" + "}\n" + "\n" + "gradle.lifecycle.beforeProject { project ->\n"
+					+ "	project.apply plugin: com.microsoft.gradle.GradlePlugin\n" + "}\n";
 			byte[] initScriptBytes = initScriptContent.getBytes();
 			byte[] initScriptDigest = getContentDigest(initScriptBytes);
 			String initScriptName = bytesToHex(initScriptDigest) + ".gradle";