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 3417e4f34a..ede344090e 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
@@ -48,6 +48,7 @@ import org.springframework.util.Assert;
  *
  * @author Dave Syer
  * @author Phillip Webb
+ * @author Jacques-Etienne Beaudet
  * @since 1.1.0
  */
 @Configuration
@@ -114,8 +115,9 @@ public class FlywayAutoConfiguration {
 			else {
 				flyway.setDataSource(this.dataSource);
 			}
-			//Explicitly set locations because the getter doesn't return a mutable value
+			// TODO: remove this line once SPR-13749 is fixed
 			flyway.setLocations(this.properties.getLocations().toArray(new String[0]));
+
 			return flyway;
 		}
 
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 47cfe3907f..0a5f137a6c 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
@@ -104,7 +104,20 @@ public class FlywayAutoConfigurationTests {
 
 	@Test
 	public void overrideLocations() throws Exception {
-		EnvironmentTestUtils.addEnvironment(this.context, "flyway.locations[0]:classpath:db/changelog",
+		EnvironmentTestUtils.addEnvironment(this.context,
+				"flyway.locations:classpath:db/changelog,classpath:db/migration");
+		registerAndRefresh(EmbeddedDataSourceConfiguration.class,
+				FlywayAutoConfiguration.class,
+				PropertyPlaceholderAutoConfiguration.class);
+		Flyway flyway = this.context.getBean(Flyway.class);
+		assertEquals("[classpath:db/changelog, classpath:db/migration]",
+				Arrays.asList(flyway.getLocations()).toString());
+	}
+
+	@Test
+	public void overrideLocationsList() throws Exception {
+		EnvironmentTestUtils.addEnvironment(this.context,
+				"flyway.locations[0]:classpath:db/changelog",
 				"flyway.locations[1]:classpath:db/migration");
 		registerAndRefresh(EmbeddedDataSourceConfiguration.class,
 				FlywayAutoConfiguration.class,