diff --git a/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfiguration.java b/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfiguration.java
index 0766747c50..2d58251b65 100644
--- a/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfiguration.java
+++ b/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfiguration.java
@@ -21,7 +21,6 @@ import javax.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
 
 import org.flywaydb.core.Flyway;
-import org.springframework.beans.factory.InitializingBean;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.autoconfigure.AutoConfigureAfter;
 import org.springframework.boot.autoconfigure.EnableAutoConfiguration;
@@ -120,6 +119,7 @@ public class FlywayAutoConfiguration {
 		}
 
 		@Bean
+		@ConditionalOnMissingBean
 		public FlywayMigrationInitializer flywayInitializer(Flyway flyway) {
 			return new FlywayMigrationInitializer(flyway, this.migrationStrategy);
 
@@ -143,32 +143,4 @@ public class FlywayAutoConfiguration {
 
 	}
 
-	/**
-	 * {@link InitializingBean} used to trigger {@link Flyway} migration via the
-	 * {@link FlywayMigrationStrategy}.
-	 */
-	private static class FlywayMigrationInitializer implements InitializingBean {
-
-		private final Flyway flyway;
-
-		private final FlywayMigrationStrategy migrationStrategy;
-
-		FlywayMigrationInitializer(Flyway flyway,
-				FlywayMigrationStrategy migrationStrategy) {
-			this.flyway = flyway;
-			this.migrationStrategy = migrationStrategy;
-		}
-
-		@Override
-		public void afterPropertiesSet() throws Exception {
-			if (this.migrationStrategy != null) {
-				this.migrationStrategy.migrate(this.flyway);
-			}
-			else {
-				this.flyway.migrate();
-			}
-		}
-
-	}
-
 }
diff --git a/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayMigrationInitializer.java b/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayMigrationInitializer.java
new file mode 100644
index 0000000000..0d0620fa1d
--- /dev/null
+++ b/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayMigrationInitializer.java
@@ -0,0 +1,78 @@
+/*
+ * Copyright 2012-2015 the original author or authors.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.springframework.boot.autoconfigure.flyway;
+
+import org.flywaydb.core.Flyway;
+import org.springframework.beans.factory.InitializingBean;
+import org.springframework.core.Ordered;
+import org.springframework.util.Assert;
+
+/**
+ * {@link InitializingBean} used to trigger {@link Flyway} migration via the
+ * {@link FlywayMigrationStrategy}.
+ *
+ * @author Phillip Webb
+ * @since 1.3.0
+ */
+public class FlywayMigrationInitializer implements InitializingBean, Ordered {
+
+	private final Flyway flyway;
+
+	private final FlywayMigrationStrategy migrationStrategy;
+
+	private int order = 0;
+
+	/**
+	 * Create a new {@link FlywayMigrationInitializer}
+	 * @param flyway the flyway instance
+	 */
+	public FlywayMigrationInitializer(Flyway flyway) {
+		this(flyway, null);
+	}
+
+	/**
+	 * Create a new {@link FlywayMigrationInitializer}
+	 * @param flyway the flyway instance
+	 * @param migrationStrategy the migration stragety or {@code null}
+	 */
+	public FlywayMigrationInitializer(Flyway flyway,
+			FlywayMigrationStrategy migrationStrategy) {
+		Assert.notNull(flyway, "Flyway must not be null");
+		this.flyway = flyway;
+		this.migrationStrategy = migrationStrategy;
+	}
+
+	@Override
+	public void afterPropertiesSet() throws Exception {
+		if (this.migrationStrategy != null) {
+			this.migrationStrategy.migrate(this.flyway);
+		}
+		else {
+			this.flyway.migrate();
+		}
+	}
+
+	@Override
+	public int getOrder() {
+		return this.order;
+	}
+
+	public void setOrder(int order) {
+		this.order = order;
+	}
+
+}
diff --git a/spring-boot-autoconfigure/src/test/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfigurationTests.java b/spring-boot-autoconfigure/src/test/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfigurationTests.java
index cd17875d85..3ea4511261 100644
--- a/spring-boot-autoconfigure/src/test/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfigurationTests.java
+++ b/spring-boot-autoconfigure/src/test/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfigurationTests.java
@@ -34,6 +34,7 @@ import org.springframework.boot.test.EnvironmentTestUtils;
 import org.springframework.context.annotation.AnnotationConfigApplicationContext;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
+import org.springframework.core.Ordered;
 import org.springframework.stereotype.Component;
 
 import static org.hamcrest.Matchers.equalTo;
@@ -161,6 +162,18 @@ public class FlywayAutoConfigurationTests {
 		this.context.getBean(MockFlywayMigrationStrategy.class).assertCalled();
 	}
 
+	@Test
+	public void customFlywayMigrationInitializer() throws Exception {
+		registerAndRefresh(CustomFlywayMigrationInitializer.class,
+				EmbeddedDataSourceConfiguration.class, FlywayAutoConfiguration.class,
+				PropertyPlaceholderAutoConfiguration.class);
+		assertNotNull(this.context.getBean(Flyway.class));
+		FlywayMigrationInitializer initializer = this.context
+				.getBean(FlywayMigrationInitializer.class);
+		assertThat(initializer.getOrder(), equalTo(Ordered.HIGHEST_PRECEDENCE));
+
+	}
+
 	private void registerAndRefresh(Class<?>... annotatedClasses) {
 		this.context.register(annotatedClasses);
 		this.context.refresh();
@@ -179,6 +192,18 @@ public class FlywayAutoConfigurationTests {
 
 	}
 
+	@Configuration
+	protected static class CustomFlywayMigrationInitializer {
+
+		@Bean
+		public FlywayMigrationInitializer flywayMigrationInitializer(Flyway flyway) {
+			FlywayMigrationInitializer initializer = new FlywayMigrationInitializer(
+					flyway);
+			initializer.setOrder(Ordered.HIGHEST_PRECEDENCE);
+			return initializer;
+		}
+	}
+
 	@Component
 	protected static class MockFlywayMigrationStrategy implements FlywayMigrationStrategy {