diff --git a/spring-data-jpa/src/main/java/org/springframework/data/jpa/repository/query/DeclaredQuery.java b/spring-data-jpa/src/main/java/org/springframework/data/jpa/repository/query/DeclaredQuery.java
index 670e030fb2..d472c06f2b 100644
--- a/spring-data-jpa/src/main/java/org/springframework/data/jpa/repository/query/DeclaredQuery.java
+++ b/spring-data-jpa/src/main/java/org/springframework/data/jpa/repository/query/DeclaredQuery.java
@@ -17,6 +17,7 @@
 
 import java.util.List;
 
+import org.springframework.expression.spel.standard.SpelExpressionParser;
 import org.springframework.lang.Nullable;
 import org.springframework.util.ObjectUtils;
 
@@ -37,7 +38,30 @@ interface DeclaredQuery {
 	 * @return a {@literal DeclaredQuery} instance even for a {@literal null} or empty argument.
 	 */
 	static DeclaredQuery of(@Nullable String query, boolean nativeQuery) {
-		return ObjectUtils.isEmpty(query) ? EmptyDeclaredQuery.EMPTY_QUERY : new StringQuery(query, nativeQuery);
+		return of(query, nativeQuery, null, null);
+	}
+
+	/**
+	 * Creates a {@literal DeclaredQuery} from a query {@literal String}.
+	 *
+	 * @param query might be {@literal null} or empty.
+	 * @param nativeQuery is a given query is native or not
+	 * @param entityMetadata metadata about the repository's related type
+	 * @param parser a {@link SpelExpressionParser} used to process potential SpEL expressions found in the query
+	 * @return a {@literal DeclaredQuery} instance even for a {@literal null} or empty argument.
+	 */
+	static DeclaredQuery of(@Nullable String query, boolean nativeQuery, @Nullable JpaEntityMetadata<?> entityMetadata,
+			@Nullable SpelExpressionParser parser) {
+
+		if (ObjectUtils.isEmpty(query)) {
+			return EmptyDeclaredQuery.EMPTY_QUERY;
+		}
+
+		if (entityMetadata != null) {
+			return new ExpressionBasedStringQuery(query, entityMetadata, parser, nativeQuery);
+		}
+
+		return new StringQuery(query, nativeQuery);
 	}
 
 	/**
diff --git a/spring-data-jpa/src/main/java/org/springframework/data/jpa/repository/query/ExpressionBasedStringQuery.java b/spring-data-jpa/src/main/java/org/springframework/data/jpa/repository/query/ExpressionBasedStringQuery.java
index 3bee9c2d48..3a71bcdff8 100644
--- a/spring-data-jpa/src/main/java/org/springframework/data/jpa/repository/query/ExpressionBasedStringQuery.java
+++ b/spring-data-jpa/src/main/java/org/springframework/data/jpa/repository/query/ExpressionBasedStringQuery.java
@@ -61,7 +61,7 @@ class ExpressionBasedStringQuery extends StringQuery {
 	 */
 	public ExpressionBasedStringQuery(String query, JpaEntityMetadata<?> metadata, SpelExpressionParser parser,
 			boolean nativeQuery) {
-		super(renderQueryIfExpressionOrReturnQuery(query, metadata, parser), nativeQuery && !containsExpression(query));
+		super(renderQueryIfExpressionOrReturnQuery(query, metadata, parser), nativeQuery);
 	}
 
 	/**
diff --git a/spring-data-jpa/src/main/java/org/springframework/data/jpa/repository/query/JpaQueryFactory.java b/spring-data-jpa/src/main/java/org/springframework/data/jpa/repository/query/JpaQueryFactory.java
index ef95696cb6..84c0edd628 100644
--- a/spring-data-jpa/src/main/java/org/springframework/data/jpa/repository/query/JpaQueryFactory.java
+++ b/spring-data-jpa/src/main/java/org/springframework/data/jpa/repository/query/JpaQueryFactory.java
@@ -34,7 +34,7 @@ enum JpaQueryFactory {
 
 	INSTANCE;
 
-	private static final SpelExpressionParser PARSER = new SpelExpressionParser();
+	static final SpelExpressionParser PARSER = new SpelExpressionParser();
 
 	/**
 	 * Creates a {@link RepositoryQuery} from the given {@link String} query.
diff --git a/spring-data-jpa/src/main/java/org/springframework/data/jpa/repository/query/JpaQueryMethod.java b/spring-data-jpa/src/main/java/org/springframework/data/jpa/repository/query/JpaQueryMethod.java
index ed566ba52c..4d838fafd0 100644
--- a/spring-data-jpa/src/main/java/org/springframework/data/jpa/repository/query/JpaQueryMethod.java
+++ b/spring-data-jpa/src/main/java/org/springframework/data/jpa/repository/query/JpaQueryMethod.java
@@ -162,7 +162,7 @@ private void assertParameterNamesInAnnotatedQuery() {
 
 		String annotatedQuery = getAnnotatedQuery();
 
-		if (!DeclaredQuery.of(annotatedQuery, this.isNativeQuery.get()).hasNamedParameter()) {
+		if (!DeclaredQuery.of(annotatedQuery, this.isNativeQuery.get(), this.getEntityInformation(), JpaQueryFactory.PARSER).hasNamedParameter()) {
 			return;
 		}
 
diff --git a/spring-data-jpa/src/test/java/org/springframework/data/jpa/repository/UserRepositoryTests.java b/spring-data-jpa/src/test/java/org/springframework/data/jpa/repository/UserRepositoryTests.java
index 9264185849..eb5d45f516 100644
--- a/spring-data-jpa/src/test/java/org/springframework/data/jpa/repository/UserRepositoryTests.java
+++ b/spring-data-jpa/src/test/java/org/springframework/data/jpa/repository/UserRepositoryTests.java
@@ -1073,6 +1073,14 @@ void shouldSupportModifyingQueryWithVarArgs() {
 		assertThat(repository.findByActiveTrue()).isEmpty();
 	}
 
+	@Test // GH-3096
+	void shouldSupportNativeQueriesWithSpEL() {
+
+		flushTestUsers();
+
+		assertThat(repository.nativeQueryWithSpEL()).containsExactly(firstUser, secondUser, thirdUser, fourthUser);
+	}
+
 	@Test // DATAJPA-405
 	void executesFinderWithOrderClauseOnly() {
 
diff --git a/spring-data-jpa/src/test/java/org/springframework/data/jpa/repository/query/ExpressionBasedStringQueryUnitTests.java b/spring-data-jpa/src/test/java/org/springframework/data/jpa/repository/query/ExpressionBasedStringQueryUnitTests.java
index af1928d506..dfea221678 100644
--- a/spring-data-jpa/src/test/java/org/springframework/data/jpa/repository/query/ExpressionBasedStringQueryUnitTests.java
+++ b/spring-data-jpa/src/test/java/org/springframework/data/jpa/repository/query/ExpressionBasedStringQueryUnitTests.java
@@ -106,7 +106,7 @@ void shouldDetectComplexNativeQueriesWithSpelAsNonNative() {
 						+ "AND (n.updatedAt >= ?#{#networkRequest.updatedTime.startDateTime}) AND (n.updatedAt <=?#{#networkRequest.updatedTime.endDateTime})",
 				metadata, SPEL_PARSER, true);
 
-		assertThat(query.isNativeQuery()).isFalse();
+		assertThat(query.isNativeQuery()).isTrue();
 	}
 
 	@Test
@@ -114,7 +114,7 @@ void shouldDetectSimpleNativeQueriesWithSpelAsNonNative() {
 
 		StringQuery query = new ExpressionBasedStringQuery("select n from #{#entityName} n", metadata, SPEL_PARSER, true);
 
-		assertThat(query.isNativeQuery()).isFalse();
+		assertThat(query.isNativeQuery()).isTrue();
 	}
 
 	@Test
diff --git a/spring-data-jpa/src/test/java/org/springframework/data/jpa/repository/sample/UserRepository.java b/spring-data-jpa/src/test/java/org/springframework/data/jpa/repository/sample/UserRepository.java
index c9a342538f..734979ecdd 100644
--- a/spring-data-jpa/src/test/java/org/springframework/data/jpa/repository/sample/UserRepository.java
+++ b/spring-data-jpa/src/test/java/org/springframework/data/jpa/repository/sample/UserRepository.java
@@ -734,6 +734,10 @@ List<String> findAllAndSortByFunctionResultNamedParameter(@Param("namedParameter
 	@Query("select u from User u where u.firstname >= (select Min(u0.firstname) from User u0)")
 	List<NameOnly> findProjectionBySubselect();
 
+	// GH-3096
+	@Query(value = "select * from SD_User as #{#entityName}", nativeQuery = true)
+	List<User> nativeQueryWithSpEL();
+
 	Window<User> findBy(OffsetScrollPosition position);
 
 	interface RolesAndFirstname {