diff --git a/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/handlers/JDTLanguageServer.java b/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/handlers/JDTLanguageServer.java
index 43d3e6b14b..ea799410f3 100644
--- a/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/handlers/JDTLanguageServer.java
+++ b/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/handlers/JDTLanguageServer.java
@@ -80,6 +80,7 @@
 import org.eclipse.jdt.ls.core.internal.lsp.ValidateDocumentParams;
 import org.eclipse.jdt.ls.core.internal.managers.ContentProviderManager;
 import org.eclipse.jdt.ls.core.internal.managers.ProjectsManager;
+import org.eclipse.jdt.ls.core.internal.managers.StandardProjectsManager;
 import org.eclipse.jdt.ls.core.internal.managers.TelemetryManager;
 import org.eclipse.jdt.ls.core.internal.preferences.PreferenceManager;
 import org.eclipse.jdt.ls.core.internal.preferences.Preferences;
@@ -301,6 +302,7 @@ public void initialized(InitializedParams params) {
 			@Override
 			public IStatus run(IProgressMonitor monitor) {
 				try {
+					StandardProjectsManager.cleanInvalidJavaProjects(monitor);
 					workspaceDiagnosticsHandler = new WorkspaceDiagnosticsHandler(JDTLanguageServer.this.client, pm, preferenceManager.getClientPreferences(), documentLifeCycleHandler);
 					workspaceDiagnosticsHandler.addResourceChangeListener();
 					classpathUpdateHandler = new ClasspathUpdateHandler(JDTLanguageServer.this.client, documentLifeCycleHandler);
diff --git a/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/managers/StandardProjectsManager.java b/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/managers/StandardProjectsManager.java
index c98897ff3c..bb93a6bd1b 100644
--- a/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/managers/StandardProjectsManager.java
+++ b/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/managers/StandardProjectsManager.java
@@ -668,6 +668,24 @@ public void projectsImported(IProgressMonitor monitor) {
 		this.preferenceManager.getPreferences().updateAnnotationNullAnalysisOptions();
 	}
 
+	public static void cleanInvalidJavaProjects(IProgressMonitor monitor) {
+		for (IJavaProject javaProject : ProjectUtils.getJavaProjects()) {
+			IProject project = javaProject.getProject();
+			if (project.equals(getDefaultProject())) {
+				continue;
+			}
+			IFile classpathFile = project.getFile(IJavaProject.CLASSPATH_FILE_NAME);
+			if (!classpathFile.exists()) {
+				try {
+					JavaLanguageServerPlugin.logInfo("The '" + project.getName() + "' project has no .classpath. Removing Java nature and builder.");
+					ProjectUtils.removeJavaNatureAndBuilder(project, monitor);
+				} catch (CoreException e) {
+					JavaLanguageServerPlugin.logException(e.getMessage(), e);
+				}
+			}
+		}
+	}
+
 	@Override
 	public void projectsBuildFinished(IProgressMonitor monitor) {
 		this.buildFinished = true;
diff --git a/org.eclipse.jdt.ls.tests/projects/maven/invalid2/LICENSE.txt b/org.eclipse.jdt.ls.tests/projects/maven/invalid2/LICENSE.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/org.eclipse.jdt.ls.tests/projects/maven/invalid2/module1/pom.xml b/org.eclipse.jdt.ls.tests/projects/maven/invalid2/module1/pom.xml
new file mode 100644
index 0000000000..7a0843a460
--- /dev/null
+++ b/org.eclipse.jdt.ls.tests/projects/maven/invalid2/module1/pom.xml
@@ -0,0 +1,30 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<parent>
+		<groupId>foo.bar</groupId>
+		<artifactId>invalid2</artifactId>
+		<version>0.0.1-SNAPSHOT</version>
+	</parent>
+	<artifactId>module1</artifactId>
+	<packaging>jar</packaging>
+
+	<build>
+        <resources>
+            <resource>
+                <targetPath>module1</targetPath>
+                <directory>../</directory>
+                <includes>
+                    <include>LICENSE.txt</include>
+                </includes>
+            </resource>
+            <resource>
+                <targetPath>module1</targetPath>
+                <directory>src/main/resources</directory>
+            </resource>
+        </resources>
+    </build>
+
+
+</project>
diff --git a/org.eclipse.jdt.ls.tests/projects/maven/invalid2/pom.xml b/org.eclipse.jdt.ls.tests/projects/maven/invalid2/pom.xml
new file mode 100644
index 0000000000..25bf24ccbc
--- /dev/null
+++ b/org.eclipse.jdt.ls.tests/projects/maven/invalid2/pom.xml
@@ -0,0 +1,19 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<groupId>foo.bar</groupId>
+	<artifactId>invalid2</artifactId>
+	<version>0.0.1-SNAPSHOT</version>
+	<packaging>pom</packaging>
+	<properties>
+		<revision>4.11</revision>
+		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+		<maven.compiler.source>17</maven.compiler.source>
+		<maven.compiler.target>17</maven.compiler.target>
+	</properties>
+	<modules>
+		<module>module1</module>
+	</modules>
+
+</project>
diff --git a/org.eclipse.jdt.ls.tests/src/org/eclipse/jdt/ls/core/internal/managers/MavenProjectImporterTest.java b/org.eclipse.jdt.ls.tests/src/org/eclipse/jdt/ls/core/internal/managers/MavenProjectImporterTest.java
index e368f674de..2b7b6892f7 100644
--- a/org.eclipse.jdt.ls.tests/src/org/eclipse/jdt/ls/core/internal/managers/MavenProjectImporterTest.java
+++ b/org.eclipse.jdt.ls.tests/src/org/eclipse/jdt/ls/core/internal/managers/MavenProjectImporterTest.java
@@ -455,6 +455,23 @@ public void testImportModulesWithSameArtifactId() throws Exception {
 		assertTrue(Arrays.stream(projects).anyMatch(p -> p.getName().equals("com.example.three-my-app")));
 	}
 
+	// https://github.com/redhat-developer/vscode-java/issues/3639
+	@Test
+	public void testInvalidProject() throws Exception {
+		try {
+			importMavenProject("invalid2");
+		} catch (Exception e) {
+			// ignore
+		}
+		IProject[] projects = ProjectUtils.getAllProjects(false);
+		assertEquals(2, projects.length); // invalid2 & module1
+		IJavaProject[] javaProjects = ProjectUtils.getJavaProjects();
+		assertEquals(1, javaProjects.length);
+		StandardProjectsManager.cleanInvalidJavaProjects(new NullProgressMonitor());
+		javaProjects = ProjectUtils.getJavaProjects();
+		assertEquals(0, javaProjects.length);
+	}
+
 	private static class MavenUpdateProjectJobSpy extends JobChangeAdapter {
 
 		int updateProjectJobCalled;