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 f0b24e1e869..b8d329e3d89 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
@@ -116,6 +116,8 @@ public class FlywayAutoConfiguration {
 
 		private final FlywayMigrationStrategy migrationStrategy;
 
+		private final List<FlywayConfigurationCustomizer> configurationCustomizers;
+
 		private final List<Callback> callbacks;
 
 		private final List<FlywayCallback> flywayCallbacks;
@@ -125,6 +127,7 @@ public class FlywayAutoConfiguration {
 				ObjectProvider<DataSource> dataSource,
 				@FlywayDataSource ObjectProvider<DataSource> flywayDataSource,
 				ObjectProvider<FlywayMigrationStrategy> migrationStrategy,
+				ObjectProvider<FlywayConfigurationCustomizer> fluentConfigurationCustomizers,
 				ObjectProvider<Callback> callbacks,
 				ObjectProvider<FlywayCallback> flywayCallbacks) {
 			this.properties = properties;
@@ -133,6 +136,8 @@ public class FlywayAutoConfiguration {
 			this.dataSource = dataSource.getIfUnique();
 			this.flywayDataSource = flywayDataSource.getIfAvailable();
 			this.migrationStrategy = migrationStrategy.getIfAvailable();
+			this.configurationCustomizers = fluentConfigurationCustomizers.orderedStream()
+					.collect(Collectors.toList());
 			this.callbacks = callbacks.orderedStream().collect(Collectors.toList());
 			this.flywayCallbacks = flywayCallbacks.orderedStream()
 					.collect(Collectors.toList());
@@ -145,6 +150,8 @@ public class FlywayAutoConfiguration {
 			checkLocationExists(dataSource);
 			configureProperties(configuration);
 			configureCallbacks(configuration);
+			this.configurationCustomizers
+					.forEach((customizer) -> customizer.customize(configuration));
 			Flyway flyway = configuration.load();
 			configureFlywayCallbacks(flyway);
 			return flyway;
diff --git a/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayConfigurationCustomizer.java b/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayConfigurationCustomizer.java
new file mode 100644
index 00000000000..991a226d251
--- /dev/null
+++ b/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayConfigurationCustomizer.java
@@ -0,0 +1,37 @@
+/*
+ * Copyright 2012-2018 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.api.configuration.FluentConfiguration;
+
+/**
+ * Callback interface that can be implemented by beans wishing to customize the flyway
+ * configuration.
+ *
+ * @author Stephane Nicoll
+ * @since 2.1.0
+ */
+@FunctionalInterface
+public interface FlywayConfigurationCustomizer {
+
+	/**
+	 * Customize the flyway configuration.
+	 * @param configuration the {@link FluentConfiguration} to customize
+	 */
+	void customize(FluentConfiguration configuration);
+
+}
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 8329c03d24e..bb1bf169ddf 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
@@ -363,6 +363,21 @@ public class FlywayAutoConfigurationTests {
 				});
 	}
 
+	@Test
+	public void configurationCustomizersAreConfiguredAndOrdered() {
+		this.contextRunner.withUserConfiguration(EmbeddedDataSourceConfiguration.class,
+				ConfigurationCustomizerConfiguration.class).run((context) -> {
+					assertThat(context).hasSingleBean(Flyway.class);
+					Flyway flyway = context.getBean(Flyway.class);
+					assertThat(flyway.getConfiguration().getConnectRetries())
+							.isEqualTo(5);
+					assertThat(flyway.getConfiguration().isIgnoreMissingMigrations())
+							.isTrue();
+					assertThat(flyway.getConfiguration().isIgnorePendingMigrations())
+							.isTrue();
+				});
+	}
+
 	@Configuration
 	protected static class FlywayDataSourceConfiguration {
 
@@ -478,4 +493,23 @@ public class FlywayAutoConfigurationTests {
 
 	}
 
+	@Configuration
+	static class ConfigurationCustomizerConfiguration {
+
+		@Bean
+		@Order(1)
+		public FlywayConfigurationCustomizer customizerOne() {
+			return (configuration) -> configuration.connectRetries(5)
+					.ignorePendingMigrations(true);
+		}
+
+		@Bean
+		@Order(0)
+		public FlywayConfigurationCustomizer customizerTwo() {
+			return (configuration) -> configuration.connectRetries(10)
+					.ignoreMissingMigrations(true);
+		}
+
+	}
+
 }
diff --git a/spring-boot-project/spring-boot-docs/src/main/asciidoc/howto.adoc b/spring-boot-project/spring-boot-docs/src/main/asciidoc/howto.adoc
index 0dad0de8136..c470e562998 100644
--- a/spring-boot-project/spring-boot-docs/src/main/asciidoc/howto.adoc
+++ b/spring-boot-project/spring-boot-docs/src/main/asciidoc/howto.adoc
@@ -2329,7 +2329,9 @@ of supported databases is available in
 
 {sc-spring-boot-autoconfigure}/flyway/FlywayProperties.{sc-ext}[`FlywayProperties`]
 provides most of Flyway's settings and a small set of additional properties that can be
-used to disable the migrations or switch off the location checking.
+used to disable the migrations or switch off the location checking. If you need more
+control over the configuration, consider registering a `FlywayConfigurationCustomizer`
+bean.
 
 Spring Boot calls `Flyway.migrate()` to perform the database migration. If you would like
 more control, provide a `@Bean` that implements