diff --git a/platform/external-system-api/src/com/intellij/openapi/externalSystem/settings/ExternalProjectSettings.java b/platform/external-system-api/src/com/intellij/openapi/externalSystem/settings/ExternalProjectSettings.java
index d8926c31ed90..2156b25ea2a3 100644
--- a/platform/external-system-api/src/com/intellij/openapi/externalSystem/settings/ExternalProjectSettings.java
+++ b/platform/external-system-api/src/com/intellij/openapi/externalSystem/settings/ExternalProjectSettings.java
@@ -15,6 +15,7 @@
  */
 package com.intellij.openapi.externalSystem.settings;
 
+import com.intellij.openapi.externalSystem.util.ExternalSystemApiUtil;
 import com.intellij.openapi.util.Comparing;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
@@ -45,7 +46,7 @@ public abstract class ExternalProjectSettings implements Comparable<ExternalProj
 
   private boolean myUseAutoImport;
   private boolean myCreateEmptyContentRootDirectories;
-  private boolean myUseQualifiedModuleNames;
+  private boolean myUseQualifiedModuleNames = !ExternalSystemApiUtil.isJavaCompatibleIde();
 
   public String getExternalProjectPath() {
     return myExternalProjectPath;
diff --git a/platform/external-system-api/src/com/intellij/openapi/externalSystem/util/ExternalSystemApiUtil.java b/platform/external-system-api/src/com/intellij/openapi/externalSystem/util/ExternalSystemApiUtil.java
index 93b8504c2d60..9769576522bd 100644
--- a/platform/external-system-api/src/com/intellij/openapi/externalSystem/util/ExternalSystemApiUtil.java
+++ b/platform/external-system-api/src/com/intellij/openapi/externalSystem/util/ExternalSystemApiUtil.java
@@ -56,6 +56,7 @@ import com.intellij.util.containers.*;
 import com.intellij.util.containers.Stack;
 import com.intellij.util.lang.UrlClassLoader;
 import com.intellij.util.ui.UIUtil;
+import org.jetbrains.annotations.ApiStatus;
 import org.jetbrains.annotations.Contract;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
@@ -71,6 +72,8 @@ import java.util.Queue;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
+import static com.intellij.util.PlatformUtils.*;
+
 /**
  * @author Denis Zhdanov
  * @since 4/1/13 1:31 PM
@@ -867,4 +870,15 @@ public class ExternalSystemApiUtil {
     //noinspection unchecked
     getSettings(project, systemId).subscribe(listener);
   }
+
+  /**
+   * DO NOT USE THIS METHOD.
+   * The method should be removed when the 'java' subsystem features will be extracted from External System API [IDEA-187832]
+   *
+   * @return check if the current IDE is compatible with the 'java' IntelliJ subsystem
+   */
+  @ApiStatus.Experimental
+  public static boolean isJavaCompatibleIde() {
+    return isIdeaUltimate() || isIdeaCommunity() || "AndroidStudio".equals(getPlatformPrefix());
+  }
 }
diff --git a/platform/external-system-impl/src/com/intellij/openapi/externalSystem/service/execution/ExternalSystemRunConfiguration.java b/platform/external-system-impl/src/com/intellij/openapi/externalSystem/service/execution/ExternalSystemRunConfiguration.java
index 134f8140fabc..38668c748cf8 100644
--- a/platform/external-system-impl/src/com/intellij/openapi/externalSystem/service/execution/ExternalSystemRunConfiguration.java
+++ b/platform/external-system-impl/src/com/intellij/openapi/externalSystem/service/execution/ExternalSystemRunConfiguration.java
@@ -450,7 +450,7 @@ public class ExternalSystemRunConfiguration extends LocatableConfigurationBase i
     @Nullable
     private String getJvmAgentSetup() throws ExecutionException {
       // todo [Vlad, IDEA-187832]: extract to `external-system-java` module
-      if(!PlatformUtils.isIntelliJ()) return null;
+      if(!ExternalSystemApiUtil.isJavaCompatibleIde()) return null;
 
       final JavaParameters extensionsJP = new JavaParameters();
       final RunConfigurationExtension[] extensions = Extensions.getExtensions(RunConfigurationExtension.EP_NAME);
diff --git a/plugins/gradle/src/org/jetbrains/plugins/gradle/GradleManager.java b/plugins/gradle/src/org/jetbrains/plugins/gradle/GradleManager.java
index 3ee7df89c6a5..77b26304ecfc 100644
--- a/plugins/gradle/src/org/jetbrains/plugins/gradle/GradleManager.java
+++ b/plugins/gradle/src/org/jetbrains/plugins/gradle/GradleManager.java
@@ -22,6 +22,10 @@ import com.intellij.execution.configurations.SearchScopeProvider;
 import com.intellij.execution.configurations.SimpleJavaParameters;
 import com.intellij.execution.testframework.sm.runner.SMTRunnerConsoleProperties;
 import com.intellij.openapi.diagnostic.Logger;
+import com.intellij.openapi.extensions.ExtensionPoint;
+import com.intellij.openapi.extensions.ExtensionPointListener;
+import com.intellij.openapi.extensions.Extensions;
+import com.intellij.openapi.extensions.impl.ExtensionPointImpl;
 import com.intellij.openapi.externalSystem.ExternalSystemAutoImportAware;
 import com.intellij.openapi.externalSystem.ExternalSystemConfigurableAware;
 import com.intellij.openapi.externalSystem.ExternalSystemManager;
@@ -60,6 +64,7 @@ import com.intellij.psi.search.GlobalSearchScope;
 import com.intellij.util.Function;
 import com.intellij.util.PathUtil;
 import com.intellij.util.PathsList;
+import com.intellij.util.containers.ContainerUtil;
 import com.intellij.util.containers.ContainerUtilRt;
 import com.intellij.util.messages.MessageBusConnection;
 import icons.GradleIcons;
@@ -82,6 +87,7 @@ import javax.swing.*;
 import java.io.File;
 import java.io.IOException;
 import java.util.*;
+import java.util.function.Predicate;
 
 import static com.intellij.openapi.util.io.FileUtil.pathsEqual;
 
@@ -111,7 +117,37 @@ public class GradleManager
       @Override
       protected List<GradleProjectResolverExtension> compute() {
         List<GradleProjectResolverExtension> result = ContainerUtilRt.newArrayList();
-        Collections.addAll(result, GradleProjectResolverExtension.EP_NAME.getExtensions());
+
+        // It's possible usecase when 'java' subsystem dependent plugins bundled with the non-java IDE using fat plugin distribution.
+        // This approach can lead to unwanted/incompatible extensions to be loaded.
+        // The workaround extensionsFilter should be removed when the IntelliJ java subsystem will become a regular plugin
+        // or those plugins will be fixed using the optional plugin dependency on 'org.jetbrains.plugins.gradle.java'
+        boolean isJavaIde = ExternalSystemApiUtil.isJavaCompatibleIde();
+        if(!isJavaIde) {
+          ExtensionPoint<GradleProjectResolverExtension> point =
+            Extensions.getRootArea().getExtensionPoint(GradleProjectResolverExtension.EP_NAME);
+          if(point instanceof ExtensionPointImpl) {
+            ((ExtensionPointImpl<GradleProjectResolverExtension>)point).removeUnloadableExtensions();
+          }
+        }
+        Set<String> javaIdeDependentExtensions = ContainerUtil.set(
+          "org.jetbrains.kotlin.idea.configuration.KotlinGradleProjectResolverExtension",
+          "org.jetbrains.kotlin.kapt.idea.KaptProjectResolverExtension",
+          "org.jetbrains.kotlin.allopen.ide.AllOpenProjectResolverExtension",
+          "org.jetbrains.kotlin.noarg.ide.NoArgProjectResolverExtension",
+          "org.jetbrains.kotlin.samWithReceiver.ide.SamWithReceiverProjectResolverExtension"
+        );
+        Predicate<GradleProjectResolverExtension> extensionsFilter = ext ->
+          isJavaIde || !javaIdeDependentExtensions.contains(ext.getClass().getName());
+
+        ExtensionPoint<GradleProjectResolverExtension> extensionPoint =
+          Extensions.getRootArea().getExtensionPoint(GradleProjectResolverExtension.EP_NAME);
+        extensionPoint.addExtensionPointListener(new ExtensionPointListener.Adapter<>());
+
+        Arrays.stream(GradleProjectResolverExtension.EP_NAME.getExtensions())
+              .filter(extensionsFilter)
+              .forEach(result::add);
+
         ExternalSystemApiUtil.orderAwareSort(result);
         return result;
       }
diff --git a/plugins/gradle/src/org/jetbrains/plugins/gradle/service/project/GradleProjectResolver.java b/plugins/gradle/src/org/jetbrains/plugins/gradle/service/project/GradleProjectResolver.java
index e7e9b0f4209e..97285d81e3f3 100644
--- a/plugins/gradle/src/org/jetbrains/plugins/gradle/service/project/GradleProjectResolver.java
+++ b/plugins/gradle/src/org/jetbrains/plugins/gradle/service/project/GradleProjectResolver.java
@@ -218,7 +218,12 @@ public class GradleProjectResolver implements ExternalSystemProjectResolver<Grad
 
       if(!resolverCtx.isPreviewMode()){
         // register classes of extra gradle project models required for extensions (e.g. com.android.builder.model.AndroidProject)
-        projectImportAction.addExtraProjectModelClasses(resolverExtension.getExtraProjectModelClasses());
+        try {
+          projectImportAction.addExtraProjectModelClasses(resolverExtension.getExtraProjectModelClasses());
+        }
+        catch (Throwable t) {
+          LOG.warn(t);
+        }
       }
 
       if (importCustomizer == null || importCustomizer.useExtraJvmArgs()) {
@@ -232,7 +237,12 @@ public class GradleProjectResolver implements ExternalSystemProjectResolver<Grad
       // collect extra command-line arguments
       executionSettings.withArguments(resolverExtension.getExtraCommandLineArgs());
       // collect tooling extensions classes
-      toolingExtensionClasses.addAll(resolverExtension.getToolingExtensionsClasses());
+      try {
+        toolingExtensionClasses.addAll(resolverExtension.getToolingExtensionsClasses());
+      }
+      catch (Throwable t) {
+        LOG.warn(t);
+      }
     }
 
     BuildActionExecuter<ProjectImportAction.AllModels> buildActionExecutor = resolverCtx.getConnection().action(projectImportAction);
diff --git a/plugins/gradle/src/org/jetbrains/plugins/gradle/settings/GradleProjectSettings.java b/plugins/gradle/src/org/jetbrains/plugins/gradle/settings/GradleProjectSettings.java
index eeb97fe8a81d..d63336fee280 100644
--- a/plugins/gradle/src/org/jetbrains/plugins/gradle/settings/GradleProjectSettings.java
+++ b/plugins/gradle/src/org/jetbrains/plugins/gradle/settings/GradleProjectSettings.java
@@ -3,6 +3,7 @@ package org.jetbrains.plugins.gradle.settings;
 
 import com.intellij.openapi.externalSystem.service.execution.ExternalSystemJdkUtil;
 import com.intellij.openapi.externalSystem.settings.ExternalProjectSettings;
+import com.intellij.openapi.externalSystem.util.ExternalSystemApiUtil;
 import com.intellij.util.SmartList;
 import com.intellij.util.ThreeState;
 import com.intellij.util.containers.ContainerUtil;
@@ -25,7 +26,7 @@ public class GradleProjectSettings extends ExternalProjectSettings {
   @Nullable private String myGradleJvm = ExternalSystemJdkUtil.USE_PROJECT_JDK;
   @Nullable private DistributionType distributionType;
   private boolean disableWrapperSourceDistributionNotification;
-  private boolean resolveModulePerSourceSet = true;
+  private boolean resolveModulePerSourceSet = ExternalSystemApiUtil.isJavaCompatibleIde();
   @Nullable private CompositeBuild myCompositeBuild;
 
   private ThreeState storeProjectFilesExternally = ThreeState.NO;