diff --git a/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfiguration.java b/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfiguration.java
index 7db159bc98..dc768f42de 100644
--- a/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfiguration.java
+++ b/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfiguration.java
@@ -251,7 +251,7 @@ public class FlywayAutoConfiguration {
 
 		/**
 		 * Additional configuration to ensure that {@link EntityManagerFactory} beans
-		 * depend on the {@code flywayInitializer} bean.
+		 * depend on any {@link FlywayMigrationInitializer} beans.
 		 */
 		@Configuration(proxyBeanMethods = false)
 		@ConditionalOnClass(LocalContainerEntityManagerFactoryBean.class)
@@ -260,14 +260,14 @@ public class FlywayAutoConfiguration {
 				extends EntityManagerFactoryDependsOnPostProcessor {
 
 			public FlywayInitializerJpaDependencyConfiguration() {
-				super("flywayInitializer");
+				super(FlywayMigrationInitializer.class);
 			}
 
 		}
 
 		/**
 		 * Additional configuration to ensure that {@link JdbcOperations} beans depend on
-		 * the {@code flywayInitializer} bean.
+		 * any {@link FlywayMigrationInitializer} beans.
 		 */
 		@Configuration(proxyBeanMethods = false)
 		@ConditionalOnClass(JdbcOperations.class)
@@ -276,14 +276,14 @@ public class FlywayAutoConfiguration {
 				extends JdbcOperationsDependsOnPostProcessor {
 
 			public FlywayInitializerJdbcOperationsDependencyConfiguration() {
-				super("flywayInitializer");
+				super(FlywayMigrationInitializer.class);
 			}
 
 		}
 
 		/**
 		 * Additional configuration to ensure that {@link NamedParameterJdbcOperations}
-		 * beans depend on the {@code flywayInitializer} bean.
+		 * beans depend on any {@link FlywayMigrationInitializer} beans.
 		 */
 		@Configuration(proxyBeanMethods = false)
 		@ConditionalOnClass(NamedParameterJdbcOperations.class)
@@ -292,7 +292,7 @@ public class FlywayAutoConfiguration {
 				extends NamedParameterJdbcOperationsDependsOnPostProcessor {
 
 			public FlywayInitializerNamedParameterJdbcOperationsDependencyConfiguration() {
-				super("flywayInitializer");
+				super(FlywayMigrationInitializer.class);
 			}
 
 		}
diff --git a/spring-boot-project/spring-boot-autoconfigure/src/test/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfigurationTests.java b/spring-boot-project/spring-boot-autoconfigure/src/test/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfigurationTests.java
index de2afb08ea..d608045913 100644
--- a/spring-boot-project/spring-boot-autoconfigure/src/test/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfigurationTests.java
+++ b/spring-boot-project/spring-boot-autoconfigure/src/test/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfigurationTests.java
@@ -304,6 +304,22 @@ class FlywayAutoConfigurationTests {
 				.run((context) -> assertThat(context).hasNotFailed());
 	}
 
+	@Test
+	void customFlywayMigrationInitializerWithJpa() {
+		this.contextRunner
+				.withUserConfiguration(EmbeddedDataSourceConfiguration.class,
+						CustomFlywayMigrationInitializerWithJpaConfiguration.class)
+				.run((context) -> assertThat(context).hasNotFailed());
+	}
+
+	@Test
+	void customFlywayMigrationInitializerWithJdbc() {
+		this.contextRunner
+				.withUserConfiguration(EmbeddedDataSourceConfiguration.class,
+						CustomFlywayMigrationInitializerWithJdbcConfiguration.class)
+				.run((context) -> assertThat(context).hasNotFailed());
+	}
+
 	@Test
 	void overrideBaselineVersionString() {
 		this.contextRunner.withUserConfiguration(EmbeddedDataSourceConfiguration.class)
@@ -531,6 +547,25 @@ class FlywayAutoConfigurationTests {
 
 	}
 
+	@Configuration(proxyBeanMethods = false)
+	static class CustomFlywayMigrationInitializerWithJpaConfiguration {
+
+		@Bean
+		FlywayMigrationInitializer customFlywayMigrationInitializer(Flyway flyway) {
+			return new FlywayMigrationInitializer(flyway);
+		}
+
+		@Bean
+		LocalContainerEntityManagerFactoryBean entityManagerFactoryBean(DataSource dataSource) {
+			Map<String, Object> properties = new HashMap<>();
+			properties.put("configured", "manually");
+			properties.put("hibernate.transaction.jta.platform", NoJtaPlatform.INSTANCE);
+			return new EntityManagerFactoryBuilder(new HibernateJpaVendorAdapter(), properties, null)
+					.dataSource(dataSource).build();
+		}
+
+	}
+
 	@Configuration(proxyBeanMethods = false)
 	static class CustomFlywayWithJpaConfiguration {
 
@@ -582,6 +617,32 @@ class FlywayAutoConfigurationTests {
 
 	}
 
+	@Configuration
+	protected static class CustomFlywayMigrationInitializerWithJdbcConfiguration {
+
+		private final DataSource dataSource;
+
+		protected CustomFlywayMigrationInitializerWithJdbcConfiguration(DataSource dataSource) {
+			this.dataSource = dataSource;
+		}
+
+		@Bean
+		public FlywayMigrationInitializer customFlywayMigrationInitializer(Flyway flyway) {
+			return new FlywayMigrationInitializer(flyway);
+		}
+
+		@Bean
+		public JdbcOperations jdbcOperations() {
+			return new JdbcTemplate(this.dataSource);
+		}
+
+		@Bean
+		public NamedParameterJdbcOperations namedParameterJdbcOperations() {
+			return new NamedParameterJdbcTemplate(this.dataSource);
+		}
+
+	}
+
 	@Component
 	static class MockFlywayMigrationStrategy implements FlywayMigrationStrategy {