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 897342e12f5d..25659cd43494 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
@@ -145,10 +145,6 @@ private DataSource configureDataSource(FluentConfiguration configuration, Flyway
 				String user = getProperty(properties::getUser, dataSourceProperties::determineUsername);
 				String password = getProperty(properties::getPassword, dataSourceProperties::determinePassword);
 				configuration.dataSource(url, user, password);
-				if (!CollectionUtils.isEmpty(properties.getInitSqls())) {
-					String initSql = StringUtils.collectionToDelimitedString(properties.getInitSqls(), "\n");
-					configuration.initSql(initSql);
-				}
 			}
 			else if (flywayDataSource != null) {
 				configuration.dataSource(flywayDataSource);
@@ -210,6 +206,9 @@ private void configureProperties(FluentConfiguration configuration, FlywayProper
 			map.from(properties.isSkipDefaultResolvers()).to(configuration::skipDefaultResolvers);
 			configureValidateMigrationNaming(configuration, properties.isValidateMigrationNaming());
 			map.from(properties.isValidateOnMigrate()).to(configuration::validateOnMigrate);
+			map.from(properties.getInitSqls()).whenNot(CollectionUtils::isEmpty)
+					.as((initSqls) -> StringUtils.collectionToDelimitedString(initSqls, "\n"))
+					.to(configuration::initSql);
 			// Pro properties
 			map.from(properties.getBatch()).whenNonNull().to(configuration::batch);
 			map.from(properties.getDryRunOutput()).whenNonNull().to(configuration::dryRunOutput);
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 b93a555b1e81..b234c3fc9997 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
@@ -502,6 +502,24 @@ void customFlywayClassLoader() {
 				});
 	}
 
+	@Test
+	void initSqlsWithDataSource() {
+		this.contextRunner.withUserConfiguration(EmbeddedDataSourceConfiguration.class)
+				.withPropertyValues("spring.flyway.init-sqls=SELECT 1").run((context) -> {
+					Flyway flyway = context.getBean(Flyway.class);
+					assertThat(flyway.getConfiguration().getInitSql()).isEqualTo("SELECT 1");
+				});
+	}
+
+	@Test
+	void initSqlsWithFlywayUrl() {
+		this.contextRunner.withPropertyValues("spring.flyway.url:jdbc:h2:mem:" + UUID.randomUUID(),
+				"spring.flyway.init-sqls=SELECT 1").run((context) -> {
+					Flyway flyway = context.getBean(Flyway.class);
+					assertThat(flyway.getConfiguration().getInitSql()).isEqualTo("SELECT 1");
+				});
+	}
+
 	@Configuration(proxyBeanMethods = false)
 	static class FlywayDataSourceConfiguration {