diff --git a/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/orm/jpa/JpaBaseConfiguration.java b/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/orm/jpa/JpaBaseConfiguration.java
index 8e50404fcc..c39d7542a2 100644
--- a/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/orm/jpa/JpaBaseConfiguration.java
+++ b/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/orm/jpa/JpaBaseConfiguration.java
@@ -19,6 +19,7 @@ package org.springframework.boot.autoconfigure.orm.jpa;
 import java.util.List;
 import java.util.Map;
 
+import javax.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
 
 import org.springframework.beans.BeansException;
@@ -105,7 +106,8 @@ public abstract class JpaBaseConfiguration implements BeanFactoryAware {
 
 	@Bean
 	@Primary
-	@ConditionalOnMissingBean
+	@ConditionalOnMissingBean({ LocalContainerEntityManagerFactoryBean.class,
+			EntityManagerFactory.class })
 	public LocalContainerEntityManagerFactoryBean entityManagerFactory(
 			EntityManagerFactoryBuilder factoryBuilder) {
 		Map<String, Object> vendorProperties = getVendorProperties();
diff --git a/spring-boot-autoconfigure/src/test/java/org/springframework/boot/autoconfigure/orm/jpa/AbstractJpaAutoConfigurationTests.java b/spring-boot-autoconfigure/src/test/java/org/springframework/boot/autoconfigure/orm/jpa/AbstractJpaAutoConfigurationTests.java
index d68309630f..3d9ae030a2 100644
--- a/spring-boot-autoconfigure/src/test/java/org/springframework/boot/autoconfigure/orm/jpa/AbstractJpaAutoConfigurationTests.java
+++ b/spring-boot-autoconfigure/src/test/java/org/springframework/boot/autoconfigure/orm/jpa/AbstractJpaAutoConfigurationTests.java
@@ -20,6 +20,7 @@ import java.lang.reflect.Field;
 import java.util.HashMap;
 import java.util.Map;
 
+import javax.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
 
 import org.hibernate.engine.transaction.jta.platform.internal.NoJtaPlatform;
@@ -153,10 +154,10 @@ public abstract class AbstractJpaAutoConfigurationTests {
 	}
 
 	@Test
-	public void usesManuallyDefinedEntityManagerFactoryBeanIfAvailable() {
+	public void usesManuallyDefinedLocalContainerEntityManagerFactoryBeanIfAvailable() {
 		EnvironmentTestUtils.addEnvironment(this.context,
 				"spring.datasource.initialize:false");
-		setupTestConfiguration(TestConfigurationWithEntityManagerFactory.class);
+		setupTestConfiguration(TestConfigurationWithLocalContainerEntityManagerFactoryBean.class);
 		this.context.refresh();
 		LocalContainerEntityManagerFactoryBean factoryBean = this.context
 				.getBean(LocalContainerEntityManagerFactoryBean.class);
@@ -164,6 +165,18 @@ public abstract class AbstractJpaAutoConfigurationTests {
 		assertThat(map.get("configured"), equalTo((Object) "manually"));
 	}
 
+	@Test
+	public void usesManuallyDefinedEntityManagerFactoryIfAvailable() {
+		EnvironmentTestUtils.addEnvironment(this.context,
+				"spring.datasource.initialize:false");
+		setupTestConfiguration(TestConfigurationWithEntityManagerFactory.class);
+		this.context.refresh();
+		EntityManagerFactory factoryBean = this.context
+				.getBean(EntityManagerFactory.class);
+		Map<String, Object> map = factoryBean.getProperties();
+		assertThat(map.get("configured"), equalTo((Object) "manually"));
+	}
+
 	@Test
 	public void usesManuallyDefinedTransactionManagerBeanIfAvailable() {
 		setupTestConfiguration(TestConfigurationWithTransactionManager.class);
@@ -218,13 +231,12 @@ public abstract class AbstractJpaAutoConfigurationTests {
 	}
 
 	@Configuration
-	protected static class TestConfigurationWithEntityManagerFactory extends
-			TestConfiguration {
+	protected static class TestConfigurationWithLocalContainerEntityManagerFactoryBean
+			extends TestConfiguration {
 
 		@Bean
 		public LocalContainerEntityManagerFactoryBean entityManagerFactory(
 				DataSource dataSource, JpaVendorAdapter adapter) {
-
 			LocalContainerEntityManagerFactoryBean factoryBean = new LocalContainerEntityManagerFactoryBean();
 			factoryBean.setJpaVendorAdapter(adapter);
 			factoryBean.setDataSource(dataSource);
@@ -235,6 +247,35 @@ public abstract class AbstractJpaAutoConfigurationTests {
 			factoryBean.setJpaPropertyMap(properties);
 			return factoryBean;
 		}
+
+	}
+
+	@Configuration
+	protected static class TestConfigurationWithEntityManagerFactory extends
+			TestConfiguration {
+
+		@Bean
+		public EntityManagerFactory entityManagerFactory(DataSource dataSource,
+				JpaVendorAdapter adapter) {
+			LocalContainerEntityManagerFactoryBean factoryBean = new LocalContainerEntityManagerFactoryBean();
+			factoryBean.setJpaVendorAdapter(adapter);
+			factoryBean.setDataSource(dataSource);
+			factoryBean.setPersistenceUnitName("manually-configured");
+			Map<String, Object> properties = new HashMap<String, Object>();
+			properties.put("configured", "manually");
+			properties.put("hibernate.transaction.jta.platform", NoJtaPlatform.INSTANCE);
+			factoryBean.setJpaPropertyMap(properties);
+			factoryBean.afterPropertiesSet();
+			return factoryBean.getObject();
+		}
+
+		@Bean
+		public PlatformTransactionManager transactionManager(EntityManagerFactory emf) {
+			JpaTransactionManager transactionManager = new JpaTransactionManager();
+			transactionManager.setEntityManagerFactory(emf);
+			return transactionManager;
+		}
+
 	}
 
 	@Configuration