diff --git a/extensions/flyway/deployment/src/main/java/io/quarkus/flyway/FlywayProcessor.java b/extensions/flyway/deployment/src/main/java/io/quarkus/flyway/FlywayProcessor.java
index 85576bebc80f36..68e4106a97feac 100644
--- a/extensions/flyway/deployment/src/main/java/io/quarkus/flyway/FlywayProcessor.java
+++ b/extensions/flyway/deployment/src/main/java/io/quarkus/flyway/FlywayProcessor.java
@@ -195,14 +195,8 @@ private Collection<String> discoverApplicationMigrations(Collection<String> loca
             LinkedHashSet<String> applicationMigrationResources = new LinkedHashSet<>();
             // Locations can be a comma separated list
             for (String location : locations) {
-                // Strip any 'classpath:' protocol prefixes because they are assumed
-                // but not recognized by ClassLoader.getResources()
-                if (location != null && location.startsWith(CLASSPATH_APPLICATION_MIGRATIONS_PROTOCOL + ':')) {
-                    location = location.substring(CLASSPATH_APPLICATION_MIGRATIONS_PROTOCOL.length() + 1);
-                    if (location.startsWith("/")) {
-                        location = location.substring(1);
-                    }
-                }
+                location = normalizeLocation(location);
+
                 Enumeration<URL> migrations = Thread.currentThread().getContextClassLoader().getResources(location);
                 while (migrations.hasMoreElements()) {
                     URL path = migrations.nextElement();
@@ -232,11 +226,33 @@ private Collection<String> discoverApplicationMigrations(Collection<String> loca
         }
     }
 
+    private String normalizeLocation(String location) {
+        if (location == null) {
+            throw new IllegalStateException("Flyway migration location may not be null.");
+        }
+
+        // Strip any 'classpath:' protocol prefixes because they are assumed
+        // but not recognized by ClassLoader.getResources()
+        if (location.startsWith(CLASSPATH_APPLICATION_MIGRATIONS_PROTOCOL + ':')) {
+            location = location.substring(CLASSPATH_APPLICATION_MIGRATIONS_PROTOCOL.length() + 1);
+            if (location.startsWith("/")) {
+                location = location.substring(1);
+            }
+        }
+        if (!location.endsWith("/")) {
+            location += "/";
+        }
+
+        return location;
+    }
+
     private Set<String> getApplicationMigrationsFromPath(final String location, final URL path)
             throws IOException, URISyntaxException {
+        Path rootPath = Paths.get(path.toURI());
+
         try (final Stream<Path> pathStream = Files.walk(Paths.get(path.toURI()))) {
             return pathStream.filter(Files::isRegularFile)
-                    .map(it -> Paths.get(location, it.getFileName().toString()).toString())
+                    .map(it -> Paths.get(location, rootPath.relativize(it).toString()).toString())
                     // we don't want windows paths here since the paths are going to be used as classpath paths anyway
                     .map(it -> it.replace('\\', '/'))
                     .peek(it -> LOGGER.debugf("Discovered path: %s", it))
diff --git a/extensions/flyway/deployment/src/test/java/io/quarkus/flyway/test/FlywayExtensionMigrateAtStartSubfolderTest.java b/extensions/flyway/deployment/src/test/java/io/quarkus/flyway/test/FlywayExtensionMigrateAtStartSubfolderTest.java
new file mode 100644
index 00000000000000..fa3d8e04c9c638
--- /dev/null
+++ b/extensions/flyway/deployment/src/test/java/io/quarkus/flyway/test/FlywayExtensionMigrateAtStartSubfolderTest.java
@@ -0,0 +1,41 @@
+package io.quarkus.flyway.test;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+
+import javax.inject.Inject;
+
+import org.flywaydb.core.Flyway;
+import org.flywaydb.core.api.MigrationInfo;
+import org.jboss.shrinkwrap.api.ShrinkWrap;
+import org.jboss.shrinkwrap.api.spec.JavaArchive;
+import org.junit.jupiter.api.DisplayName;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.RegisterExtension;
+
+import io.quarkus.test.QuarkusUnitTest;
+
+public class FlywayExtensionMigrateAtStartSubfolderTest {
+    // Quarkus built object
+    @Inject
+    Flyway flyway;
+
+    @RegisterExtension
+    static final QuarkusUnitTest config = new QuarkusUnitTest()
+            .setArchiveProducer(() -> ShrinkWrap.create(JavaArchive.class)
+                    .addAsResource("db/migration-subfolder/subfolder/V1.0.0__Quarkus.sql")
+                    .addAsResource("migrate-at-start-subfolder-config.properties", "application.properties"));
+
+    @Test
+    @DisplayName("Migrates at start correctly")
+    public void testFlywayConfigInjection() {
+        MigrationInfo migrationInfo = flyway.info().current();
+        assertNotNull(migrationInfo, "No Flyway migration was executed");
+
+        String currentVersion = migrationInfo
+                .getVersion()
+                .toString();
+        // Expected to be 1.0.0 as migration runs at start
+        assertEquals("1.0.0", currentVersion);
+    }
+}
diff --git a/extensions/flyway/deployment/src/test/resources/db/migration-subfolder/subfolder/V1.0.0__Quarkus.sql b/extensions/flyway/deployment/src/test/resources/db/migration-subfolder/subfolder/V1.0.0__Quarkus.sql
new file mode 100644
index 00000000000000..241cad5122ccb0
--- /dev/null
+++ b/extensions/flyway/deployment/src/test/resources/db/migration-subfolder/subfolder/V1.0.0__Quarkus.sql
@@ -0,0 +1,5 @@
+CREATE TABLE quarked_flyway
+(
+    id   INT,
+    name VARCHAR(20)
+);
\ No newline at end of file
diff --git a/extensions/flyway/deployment/src/test/resources/migrate-at-start-subfolder-config.properties b/extensions/flyway/deployment/src/test/resources/migrate-at-start-subfolder-config.properties
new file mode 100644
index 00000000000000..c57bf8416f737f
--- /dev/null
+++ b/extensions/flyway/deployment/src/test/resources/migrate-at-start-subfolder-config.properties
@@ -0,0 +1,8 @@
+quarkus.datasource.db-kind=h2
+quarkus.datasource.username=sa
+quarkus.datasource.password=sa
+quarkus.datasource.jdbc.url=jdbc:h2:tcp://localhost/mem:test-quarkus-migrate-at-start-subfolder;DB_CLOSE_DELAY=-1
+
+# Flyway config properties
+quarkus.flyway.locations=db/migration-subfolder
+quarkus.flyway.migrate-at-start=true