diff --git a/documentation/src/main/asciidoc/advanced-features.asciidoc b/documentation/src/main/asciidoc/advanced-features.asciidoc
index 118c5c9e09f..472719a0ebf 100644
--- a/documentation/src/main/asciidoc/advanced-features.asciidoc
+++ b/documentation/src/main/asciidoc/advanced-features.asciidoc
@@ -252,6 +252,10 @@ have ideas, or just to let us know how you're using this API.
 It is technically possible to store the information of more than one entity into a single Lucene
 index. There are two ways to accomplish this:
 
+[WARNING]
+====
+Support for indexing multiple entity types in the same index is deprecated and is going to be removed in Hibernate Search 6.
+====
 
 * Configuring the underlying directory providers to point to the same physical index directory.
 In practice, you set the property `hibernate.search.[fully qualified entity name].indexName` to the
diff --git a/engine/src/main/java/org/hibernate/search/spi/SearchIntegratorBuilder.java b/engine/src/main/java/org/hibernate/search/spi/SearchIntegratorBuilder.java
index 0d4e3507e3d..cc3c1c4ac7f 100644
--- a/engine/src/main/java/org/hibernate/search/spi/SearchIntegratorBuilder.java
+++ b/engine/src/main/java/org/hibernate/search/spi/SearchIntegratorBuilder.java
@@ -467,6 +467,15 @@ else if ( metadataProvider.containsSearchMetadata( mappedClassIdentifier ) ) {
 				documentBuildersContainedEntities
 		);
 
+		if ( HibernateSearch6DeprecationHelper.isWarningEnabled( searchConfiguration.getProperties() ) ) {
+			for ( IndexManager indexManager : indexesFactory.getIndexManagers() ) {
+				IndexedTypeSet indexedTypes = indexManager.getContainedTypes();
+				if ( indexedTypes.size() > 1 ) {
+					log.multipleTypesInSingleIndex( indexManager.getIndexName(), indexedTypes );
+				}
+			}
+		}
+
 		factoryState.addFilterDefinitions( configContext.initFilters() );
 		factoryState.addIntegrations( configContext.initIntegrations( indexesFactory ) );
 	}
diff --git a/engine/src/main/java/org/hibernate/search/util/logging/impl/Log.java b/engine/src/main/java/org/hibernate/search/util/logging/impl/Log.java
index 450c8fbcd1e..c5aad1d2ad5 100644
--- a/engine/src/main/java/org/hibernate/search/util/logging/impl/Log.java
+++ b/engine/src/main/java/org/hibernate/search/util/logging/impl/Log.java
@@ -35,6 +35,7 @@
 import org.hibernate.search.exception.EmptyQueryException;
 import org.hibernate.search.exception.SearchException;
 import org.hibernate.search.spi.IndexedTypeIdentifier;
+import org.hibernate.search.spi.IndexedTypeSet;
 import org.hibernate.search.store.DirectoryProvider;
 import org.jboss.logging.Logger.Level;
 import org.jboss.logging.annotations.Cause;
@@ -1031,4 +1032,12 @@ public interface Log extends BaseHibernateSearchLogger {
 			+ " and cannot be used with any other technology (Elasticsearch in particular)."
 			+ " Analyzer reference: %s")
 	SearchException invalidConversionFromLuceneAnalyzer(LuceneAnalyzerReference reference, @Cause Exception cause);
+
+	@LogMessage(level = Level.WARN)
+	@Message(id = 355, value = "Index '%1$s' is assigned to multiple entity types: %2$s"
+			+ " Support for indexing multiple entity types in the same index is going to be removed in Hibernate Search 6."
+			+ " To assign a dedicated index to each type in a entity class hierarchy,"
+			+ " use @Indexed(index = \"someUniqueName\") on non-root classes." )
+	void multipleTypesInSingleIndex(String indexName, IndexedTypeSet indexedTypes);
+
 }
diff --git a/engine/src/test/java/org/hibernate/search/test/configuration/MultipleTypesInSingleIndexDeprecationTest.java b/engine/src/test/java/org/hibernate/search/test/configuration/MultipleTypesInSingleIndexDeprecationTest.java
new file mode 100644
index 00000000000..a49ce2d4876
--- /dev/null
+++ b/engine/src/test/java/org/hibernate/search/test/configuration/MultipleTypesInSingleIndexDeprecationTest.java
@@ -0,0 +1,72 @@
+/*
+ * Hibernate Search, full-text search for your domain model
+ *
+ * License: GNU Lesser General Public License (LGPL), version 2.1 or later
+ * See the lgpl.txt file in the root directory or <http://www.gnu.org/licenses/lgpl-2.1.html>.
+ */
+package org.hibernate.search.test.configuration;
+
+import org.hibernate.search.annotations.DocumentId;
+import org.hibernate.search.annotations.Field;
+import org.hibernate.search.annotations.Indexed;
+import org.hibernate.search.test.util.impl.ExpectedLog4jLog;
+import org.hibernate.search.testsupport.TestForIssue;
+import org.hibernate.search.testsupport.junit.SearchIntegratorResource;
+import org.hibernate.search.testsupport.setup.SearchConfigurationForTest;
+
+import org.junit.Rule;
+import org.junit.Test;
+
+import org.apache.log4j.Level;
+import org.hamcrest.CoreMatchers;
+
+@TestForIssue(jiraKey = "HSEARCH-4336")
+public class MultipleTypesInSingleIndexDeprecationTest {
+
+	@Rule
+	public final SearchIntegratorResource integratorResource = new SearchIntegratorResource();
+
+	@Rule
+	public ExpectedLog4jLog logged = ExpectedLog4jLog.create();
+
+	@Test
+	public void default_warning() {
+		SearchConfigurationForTest cfg = new SearchConfigurationForTest();
+		cfg.addClass( RootEntityType.class );
+		cfg.addClass( DerivedEntityType.class );
+
+		logged.expectEvent( Level.WARN, CoreMatchers.nullValue(),
+				"Index 'myIndex' is assigned to multiple entity types:",
+				RootEntityType.class.getName(),
+				DerivedEntityType.class.getName(),
+				"Support for indexing multiple entity types in the same index is going to be removed in Hibernate Search 6" );
+
+		integratorResource.create( cfg );
+	}
+
+	@Test
+	public void property_noWarning() {
+		SearchConfigurationForTest cfg = new SearchConfigurationForTest();
+		cfg.addClass( RootEntityType.class );
+		cfg.addClass( DerivedEntityType.class );
+
+		cfg.addProperty( "hibernate.search.v6_migration.deprecation_warnings", "false" );
+
+		logged.expectLevel( Level.WARN ).never();
+
+		integratorResource.create( cfg );
+	}
+
+	@Indexed(index = "myIndex")
+	public static class RootEntityType {
+		@DocumentId
+		private long id;
+		@Field
+		private String field;
+	}
+
+	@Indexed
+	public static class DerivedEntityType extends RootEntityType {
+	}
+
+}