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 6365e655c5f8..f155ed2c8c18 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
@@ -125,7 +125,7 @@ public Flyway flyway(FlywayProperties properties, DataSourceProperties dataSourc
 				ObjectProvider<JavaMigration> javaMigrations, ObjectProvider<Callback> callbacks) {
 			FluentConfiguration configuration = new FluentConfiguration(resourceLoader.getClassLoader());
 			DataSource dataSourceToMigrate = configureDataSource(configuration, properties, dataSourceProperties,
-					flywayDataSource.getIfAvailable(), dataSource.getIfAvailable());
+					flywayDataSource.getIfAvailable(), dataSource.getIfUnique());
 			checkLocationExists(dataSourceToMigrate, properties, resourceLoader);
 			configureProperties(configuration, properties);
 			List<Callback> orderedCallbacks = callbacks.orderedStream().collect(Collectors.toList());
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 a1e2c9b8ee91..d07a732b0eca 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
@@ -77,6 +77,7 @@
  * @author Stephane Nicoll
  * @author Dominic Gunn
  * @author András Deák
+ * @author Takaaki Shimbo
  */
 @ExtendWith(OutputCaptureExtension.class)
 class FlywayAutoConfigurationTests {
@@ -162,6 +163,15 @@ void flywayDataSourceWithoutDataSourceAutoConfiguration() {
 		});
 	}
 
+	@Test
+	void flywayMultipleDataSources() {
+		this.contextRunner.withUserConfiguration(FlywayMultipleDataSourcesConfiguration.class).run((context) -> {
+			assertThat(context).hasSingleBean(Flyway.class);
+			assertThat(context.getBean(Flyway.class).getConfiguration().getDataSource())
+					.isEqualTo(context.getBean("flywayDataSource"));
+		});
+	}
+
 	@Test
 	void schemaManagementProviderDetectsDataSource() {
 		this.contextRunner
@@ -509,6 +519,27 @@ DataSource flywayDataSource() {
 
 	}
 
+	@Configuration(proxyBeanMethods = false)
+	static class FlywayMultipleDataSourcesConfiguration {
+
+		@Bean
+		DataSource mainDataSource() {
+			return DataSourceBuilder.create().url("jdbc:hsqldb:mem:main").username("sa").build();
+		}
+
+		@Bean
+		DataSource secondlyDataSource() {
+			return DataSourceBuilder.create().url("jdbc:hsqldb:mem:secondly").username("sa").build();
+		}
+
+		@FlywayDataSource
+		@Bean
+		DataSource flywayDataSource(DataSource mainDataSource) {
+			return mainDataSource;
+		}
+
+	}
+
 	@Configuration(proxyBeanMethods = false)
 	static class FlywayJavaMigrationsConfiguration {