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 c73d979bd4..3e8edddd8f 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
@@ -119,10 +119,9 @@ public class FlywayAutoConfiguration {
 			configureProperties(configuration, properties);
 			List<Callback> orderedCallbacks = callbacks.orderedStream().collect(Collectors.toList());
 			configureCallbacks(configuration, orderedCallbacks);
-			fluentConfigurationCustomizers.orderedStream().forEach((customizer) -> customizer.customize(configuration));
-			configureFlywayCallbacks(configuration, orderedCallbacks);
 			List<JavaMigration> migrations = javaMigrations.stream().collect(Collectors.toList());
 			configureJavaMigrations(configuration, migrations);
+			fluentConfigurationCustomizers.orderedStream().forEach((customizer) -> customizer.customize(configuration));
 			return configuration.load();
 		}
 
@@ -245,12 +244,6 @@ public class FlywayAutoConfiguration {
 			}
 		}
 
-		private void configureFlywayCallbacks(FluentConfiguration flyway, List<Callback> callbacks) {
-			if (!callbacks.isEmpty()) {
-				flyway.callbacks(callbacks.toArray(new Callback[0]));
-			}
-		}
-
 		private void configureJavaMigrations(FluentConfiguration flyway, List<JavaMigration> migrations) {
 			if (!migrations.isEmpty()) {
 				flyway.javaMigrations(migrations.toArray(new JavaMigration[0]));
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 a5297381c8..9f30802049 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
@@ -467,6 +467,17 @@ class FlywayAutoConfigurationTests {
 				});
 	}
 
+	@Test
+	void callbackAndMigrationBeansAreAppliedToConfigurationBeforeCustomizersAreCalled() {
+		this.contextRunner
+				.withUserConfiguration(EmbeddedDataSourceConfiguration.class, FlywayJavaMigrationsConfiguration.class,
+						CallbackConfiguration.class)
+				.withBean(FlywayConfigurationCustomizer.class, () -> (configuration) -> {
+					assertThat(configuration.getCallbacks()).isNotEmpty();
+					assertThat(configuration.getJavaMigrations()).isNotEmpty();
+				}).run((context) -> assertThat(context).hasNotFailed());
+	}
+
 	@Test
 	void batchIsCorrectlyMapped() {
 		this.contextRunner.withUserConfiguration(EmbeddedDataSourceConfiguration.class)