diff --git a/spring-modulith-runtime/src/main/java/org/springframework/modulith/runtime/flyway/HasMigrationFiles.java b/spring-modulith-runtime/src/main/java/org/springframework/modulith/runtime/flyway/HasMigrationFiles.java
index c2759378d..8424bb0fb 100644
--- a/spring-modulith-runtime/src/main/java/org/springframework/modulith/runtime/flyway/HasMigrationFiles.java
+++ b/spring-modulith-runtime/src/main/java/org/springframework/modulith/runtime/flyway/HasMigrationFiles.java
@@ -63,9 +63,10 @@ public boolean shouldMigrate(ApplicationModuleIdentifier identifier, Flyway flyw
 	}
 
 	private int getNumberOfMigrationFiles(Location location, ApplicationModuleIdentifier identifier) {
+		var asPath = identifier.toString().replace('.', '/');
 
 		try {
-			return resolver.getResources("%s/%s/*".formatted(location, identifier.toString())).length;
+			return resolver.getResources("%s/%s/*".formatted(location, asPath)).length;
 		} catch (FileNotFoundException e) {
 			return 0;
 		} catch (IOException e) {
diff --git a/spring-modulith-runtime/src/test/java/org/springframework/modulith/runtime/flyway/SpringModulithFlywayCustomizerUnitTests.java b/spring-modulith-runtime/src/test/java/org/springframework/modulith/runtime/flyway/SpringModulithFlywayCustomizerUnitTests.java
index 65b1ddbdb..b90012ca6 100644
--- a/spring-modulith-runtime/src/test/java/org/springframework/modulith/runtime/flyway/SpringModulithFlywayCustomizerUnitTests.java
+++ b/spring-modulith-runtime/src/test/java/org/springframework/modulith/runtime/flyway/SpringModulithFlywayCustomizerUnitTests.java
@@ -100,6 +100,25 @@ void dropModulesWithoutMigrations() {
 				});
 	}
 
+	@Test // GH-1962
+	void retainsModulesWithMigrationsForDottedIdentifiers() {
+
+		var identifiers = ApplicationModuleIdentifiers.of(List.of(
+				ApplicationModuleIdentifier.of("fully.qualified")));
+
+		var filter = new HasMigrationFiles(new PathMatchingResourcePatternResolver());
+
+		var result = new SpringModulithFlywayCustomizer(Flyway.configure().load(), filter)
+				.augment(identifiers)
+				.toList();
+
+		assertThat(result).hasSize(2);
+
+		assertThat(result.get(1).getConfiguration().getLocations())
+				.extracting(Location::toString)
+				.containsExactly("classpath:db/migration/fully/qualified");
+	}
+
 	@Builder
 	@ToString
 	@RequiredArgsConstructor
diff --git a/spring-modulith-runtime/src/test/resources/db/migration/fully/qualified/V1__init.sql b/spring-modulith-runtime/src/test/resources/db/migration/fully/qualified/V1__init.sql
new file mode 100644
index 000000000..319ed7cd5
--- /dev/null
+++ b/spring-modulith-runtime/src/test/resources/db/migration/fully/qualified/V1__init.sql
@@ -0,0 +1 @@
+-- nested module migration