diff --git a/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/NativeImageResourceProvider.java b/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/NativeImageResourceProvider.java
index 7970d9aad67..47dc32b64d0 100644
--- a/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/NativeImageResourceProvider.java
+++ b/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/NativeImageResourceProvider.java
@@ -145,7 +145,7 @@ class NativeImageResourceProvider implements ResourceProvider {
 
 	private Resource[] getResources(PathMatchingResourcePatternResolver resolver, Location location, Resource root) {
 		try {
-			return resolver.getResources(root.getURI() + "/*");
+			return resolver.getResources(root.getURI() + "/**/*");
 		}
 		catch (IOException ex) {
 			throw new UncheckedIOException("Failed to list resources for " + location.getDescriptor(), ex);
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 16952805132..56ce9402515 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
@@ -968,6 +968,8 @@ class FlywayAutoConfigurationTests {
 		new FlywayAutoConfigurationRuntimeHints().registerHints(runtimeHints, getClass().getClassLoader());
 		assertThat(RuntimeHintsPredicates.resource().forResource("db/migration/")).accepts(runtimeHints);
 		assertThat(RuntimeHintsPredicates.resource().forResource("db/migration/V1__init.sql")).accepts(runtimeHints);
+		assertThat(RuntimeHintsPredicates.resource().forResource("db/migration/nested/V2__users.sql"))
+			.accepts(runtimeHints);
 	}
 
 	@Test
diff --git a/spring-boot-project/spring-boot-autoconfigure/src/test/java/org/springframework/boot/autoconfigure/flyway/NativeImageResourceProviderCustomizerTests.java b/spring-boot-project/spring-boot-autoconfigure/src/test/java/org/springframework/boot/autoconfigure/flyway/NativeImageResourceProviderCustomizerTests.java
index 083e5b606ad..9563a85082d 100644
--- a/spring-boot-project/spring-boot-autoconfigure/src/test/java/org/springframework/boot/autoconfigure/flyway/NativeImageResourceProviderCustomizerTests.java
+++ b/spring-boot-project/spring-boot-autoconfigure/src/test/java/org/springframework/boot/autoconfigure/flyway/NativeImageResourceProviderCustomizerTests.java
@@ -25,6 +25,7 @@ import org.flywaydb.core.internal.resource.NoopResourceProvider;
 import org.junit.jupiter.api.Test;
 
 import org.springframework.boot.testsupport.classpath.resources.WithResource;
+import org.springframework.boot.testsupport.classpath.resources.WithResources;
 
 import static org.assertj.core.api.Assertions.assertThat;
 
@@ -56,6 +57,19 @@ class NativeImageResourceProviderCustomizerTests {
 		assertThat(migrations).containsExactly(migration);
 	}
 
+	@Test
+	@WithResources({ @WithResource(name = "db/migration/V1__init.sql"),
+			@WithResource(name = "db/migration/nested/V2__users.sql") })
+	void nativeImageResourceProviderShouldFindNestedMigrations() {
+		FluentConfiguration configuration = new FluentConfiguration();
+		this.customizer.customize(configuration);
+		ResourceProvider resourceProvider = configuration.getResourceProvider();
+		Collection<LoadableResource> migrations = resourceProvider.getResources("V", new String[] { ".sql" });
+		LoadableResource v1 = resourceProvider.getResource("V1__init.sql");
+		LoadableResource v2 = resourceProvider.getResource("nested/V2__users.sql");
+		assertThat(migrations).containsExactly(v1, v2);
+	}
+
 	@Test
 	void shouldBackOffOnCustomResourceProvider() {
 		FluentConfiguration configuration = new FluentConfiguration();