diff --git a/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/managers/GradleBuildSupport.java b/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/managers/GradleBuildSupport.java
index 0543dd66c3..e7ec9e9961 100644
--- a/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/managers/GradleBuildSupport.java
+++ b/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/managers/GradleBuildSupport.java
@@ -27,6 +27,7 @@
 import org.eclipse.buildship.core.GradleBuild;
 import org.eclipse.buildship.core.GradleCore;
 import org.eclipse.buildship.core.internal.CorePlugin;
+import org.eclipse.buildship.core.internal.DefaultGradleBuild;
 import org.eclipse.buildship.core.internal.launch.GradleClasspathProvider;
 import org.eclipse.buildship.core.internal.preferences.PersistentModel;
 import org.eclipse.buildship.core.internal.util.file.FileUtils;
@@ -106,7 +107,17 @@ public void update(IProject project, boolean force, IProgressMonitor monitor) th
 					|| (settingsFile.exists() && JavaLanguageServerPlugin.getDigestStore().updateDigest(settingsFile.toPath()))
 					|| (buildKtsFile.exists() && JavaLanguageServerPlugin.getDigestStore().updateDigest(buildKtsFile.toPath()))
 					|| (settingsKtsFile.exists() && JavaLanguageServerPlugin.getDigestStore().updateDigest(settingsKtsFile.toPath()));
-			if (isRoot || shouldUpdate) {
+			// https://github.com/redhat-developer/vscode-java/issues/3893
+			shouldUpdate = isRoot || shouldUpdate;
+			if (!shouldUpdate) {
+				if (force && gradleBuild instanceof DefaultGradleBuild defaultGradleBuild) {
+					org.eclipse.buildship.core.internal.configuration.BuildConfiguration gradleConfig = defaultGradleBuild.getBuildConfig();
+					if (!gradleConfig.isAutoSync()) {
+						shouldUpdate = true;
+					}
+				}
+			}
+			if (shouldUpdate) {
 				gradleBuild.synchronize(monitor);
 				syncAnnotationProcessingConfiguration(gradleBuild, monitor);
 			}
diff --git a/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/managers/GradlePreferenceChangeListener.java b/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/managers/GradlePreferenceChangeListener.java
index 7628feb686..35388f2ae1 100644
--- a/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/managers/GradlePreferenceChangeListener.java
+++ b/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/managers/GradlePreferenceChangeListener.java
@@ -17,6 +17,9 @@
 import java.nio.file.Paths;
 import java.util.Objects;
 
+import org.eclipse.buildship.core.BuildConfiguration;
+import org.eclipse.buildship.core.GradleBuild;
+import org.eclipse.buildship.core.GradleCore;
 import org.eclipse.buildship.core.GradleDistribution;
 import org.eclipse.buildship.core.WrapperGradleDistribution;
 import org.eclipse.buildship.core.internal.CorePlugin;
@@ -31,6 +34,7 @@
 import org.eclipse.jdt.ls.core.internal.ProjectUtils;
 import org.eclipse.jdt.ls.core.internal.preferences.IPreferencesChangeListener;
 import org.eclipse.jdt.ls.core.internal.preferences.Preferences;
+import org.eclipse.jdt.ls.core.internal.preferences.Preferences.FeatureStatus;
 import org.eclipse.jdt.ls.internal.gradle.checksums.ValidationResult;
 import org.eclipse.jdt.ls.internal.gradle.checksums.WrapperValidator;
 
@@ -79,6 +83,20 @@ public void preferencesChange(Preferences oldPreferences, Preferences newPrefere
 					}
 				}
 			}
+			boolean updateBuildConfigurationChanged = !Objects.equals(oldPreferences.getUpdateBuildConfigurationStatus(), newPreferences.getUpdateBuildConfigurationStatus());
+			if (updateBuildConfigurationChanged) {
+				if (newPreferences.getUpdateBuildConfigurationStatus().equals(FeatureStatus.automatic)) {
+					for (IProject project : ProjectUtils.getGradleProjects()) {
+						ProjectConfiguration configuration = CorePlugin.configurationManager().loadProjectConfiguration(project);
+						if (!configuration.getBuildConfiguration().isAutoSync()) {
+							String projectPath = project.getLocation().toFile().getAbsolutePath();
+							BuildConfiguration buildConfiguration = GradleProjectImporter.getBuildConfiguration(Paths.get(projectPath));
+							GradleBuild gradleBuild = GradleCore.getWorkspace().createBuild(buildConfiguration);
+							gradleBuild.synchronize(new NullProgressMonitor());
+						}
+					}
+				}
+			}
 		}
 	}
 
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 5eb3f89bfb..b38e3a33b3 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
@@ -40,6 +40,9 @@
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
+import org.eclipse.buildship.core.GradleBuild;
+import org.eclipse.buildship.core.GradleCore;
+import org.eclipse.buildship.core.internal.DefaultGradleBuild;
 import org.eclipse.core.internal.preferences.EclipsePreferences;
 import org.eclipse.core.resources.IFile;
 import org.eclipse.core.resources.IFolder;
@@ -263,7 +266,22 @@ public void fileChanged(String uriString, CHANGE_TYPE changeType) {
 								// The sync task is handled by Buildship when sync.auto is turned on,
 								// except for the annotation processing configuration updating.
 								// See https://github.com/redhat-developer/vscode-java/issues/2673
-								GradleBuildSupport.syncAnnotationProcessingConfiguration(project, new NullProgressMonitor());
+								// See https://github.com/redhat-developer/vscode-java/issues/3893
+								Optional<GradleBuild> build = GradleCore.getWorkspace().getBuild(project);
+								boolean syncAnnotationProcessing = true;
+								if (build.isPresent()) {
+									GradleBuild gradleBuild = build.get();
+									if (gradleBuild instanceof DefaultGradleBuild defaultGradleBuild) {
+										org.eclipse.buildship.core.internal.configuration.BuildConfiguration gradleConfig = defaultGradleBuild.getBuildConfig();
+										if (!gradleConfig.isAutoSync()) {
+											updateProject(project, true);
+											syncAnnotationProcessing = false;
+										}
+									}
+								}
+								if (syncAnnotationProcessing) {
+									GradleBuildSupport.syncAnnotationProcessingConfiguration(project, new NullProgressMonitor());
+								}
 								return;
 							}
 							updateProject(project, true);
diff --git a/org.eclipse.jdt.ls.tests/src/org/eclipse/jdt/ls/core/internal/managers/GradleBuildSupportTest.java b/org.eclipse.jdt.ls.tests/src/org/eclipse/jdt/ls/core/internal/managers/GradleBuildSupportTest.java
index 9f19f55ab4..7b5282a586 100644
--- a/org.eclipse.jdt.ls.tests/src/org/eclipse/jdt/ls/core/internal/managers/GradleBuildSupportTest.java
+++ b/org.eclipse.jdt.ls.tests/src/org/eclipse/jdt/ls/core/internal/managers/GradleBuildSupportTest.java
@@ -15,12 +15,22 @@
 import static org.eclipse.jdt.ls.core.internal.ResourceUtils.getContent;
 import static org.eclipse.jdt.ls.core.internal.ResourceUtils.setContent;
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
 
+import java.io.InputStream;
 import java.net.URI;
+import java.util.List;
 
 import org.eclipse.core.resources.IFile;
 import org.eclipse.core.resources.IProject;
+import org.eclipse.jdt.core.IJavaProject;
+import org.eclipse.jdt.core.IType;
+import org.eclipse.jdt.core.JavaCore;
 import org.eclipse.jdt.ls.core.internal.ProjectUtils;
+import org.eclipse.jdt.ls.core.internal.WorkspaceHelper;
+import org.eclipse.jdt.ls.core.internal.managers.ProjectsManager.CHANGE_TYPE;
+import org.eclipse.jdt.ls.core.internal.preferences.Preferences.FeatureStatus;
 import org.junit.Test;
 
 /**
@@ -62,4 +72,37 @@ public void testUpdate() throws Exception {
 		assertEquals("1.8", ProjectUtils.getJavaSourceLevel(project));
 	}
 
+	// https://github.com/redhat-developer/vscode-java/issues/3893
+	@Test
+	public void testUpdateModule() throws Exception {
+		FeatureStatus oldSettings = preferenceManager.getPreferences().getUpdateBuildConfigurationStatus();
+		try {
+			preferenceManager.getPreferences().setUpdateBuildConfigurationStatus(FeatureStatus.disabled);
+			List<IProject> projects = importProjects("gradle/sample");
+			assertEquals(2, projects.size()); // app, sample
+			IProject root = WorkspaceHelper.getProject("sample");
+			assertIsGradleProject(root);
+			IProject project = WorkspaceHelper.getProject("app");
+			assertIsGradleProject(project);
+			assertIsJavaProject(project);
+			IJavaProject javaProject = JavaCore.create(project);
+			IType type = javaProject.findType("org.apache.commons.lang3.StringUtils");
+			assertNull(type);
+			IFile build2 = project.getFile("/build.gradle2");
+			InputStream contents = build2.getContents();
+			IFile build = project.getFile("/build.gradle");
+			build.setContents(contents, true, false, null);
+			projectsManager.fileChanged(build.getRawLocation().toPath().toUri().toString(), CHANGE_TYPE.CHANGED);
+			waitForBackgroundJobs();
+			type = javaProject.findType("org.apache.commons.lang3.StringUtils");
+			assertNull(type);
+			projectsManager.updateProject(project, true);
+			waitForBackgroundJobs();
+			type = javaProject.findType("org.apache.commons.lang3.StringUtils");
+			assertNotNull(type);
+		} finally {
+			preferenceManager.getPreferences().setUpdateBuildConfigurationStatus(oldSettings);
+		}
+	}
+
 }