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 d04388a3b86e7..ef92094d9ff23 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
@@ -12,7 +12,6 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
-import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Enumeration;
 import java.util.HashMap;
@@ -103,7 +102,7 @@ void build(BuildProducer<FeatureBuildItem> featureProducer,
 
         Collection<String> dataSourceNames = getDataSourceNames(jdbcDataSourceBuildItems);
 
-        List<String> applicationMigrations = discoverApplicationMigrations(getMigrationLocations(dataSourceNames));
+        Collection<String> applicationMigrations = discoverApplicationMigrations(getMigrationLocations(dataSourceNames));
         recorder.setApplicationMigrationFiles(applicationMigrations);
 
         Set<Class<?>> javaMigrationClasses = new HashSet<>();
@@ -196,15 +195,19 @@ private Collection<String> getMigrationLocations(Collection<String> dataSourceNa
         return migrationLocations;
     }
 
-    private List<String> discoverApplicationMigrations(Collection<String> locations) throws IOException, URISyntaxException {
+    private Collection<String> discoverApplicationMigrations(Collection<String> locations)
+            throws IOException, URISyntaxException {
         try {
-            List<String> applicationMigrationResources = new ArrayList<>();
+            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);
+                    }
                 }
                 Enumeration<URL> migrations = Thread.currentThread().getContextClassLoader().getResources(location);
                 while (migrations.hasMoreElements()) {
diff --git a/integration-tests/flyway/src/main/resources/application.properties b/integration-tests/flyway/src/main/resources/application.properties
index c755b65541234..6e99424fe1822 100644
--- a/integration-tests/flyway/src/main/resources/application.properties
+++ b/integration-tests/flyway/src/main/resources/application.properties
@@ -11,7 +11,7 @@ quarkus.datasource.jdbc.url=jdbc:h2:tcp://localhost/mem:test_quarkus;DB_CLOSE_DE
 quarkus.flyway.connect-retries=10
 quarkus.flyway.schemas=TEST_SCHEMA
 quarkus.flyway.table=flyway_quarkus_history
-quarkus.flyway.locations=db/location1,classpath:db/location2
+quarkus.flyway.locations=db/location1,classpath:db/location2,classpath:/db/location4
 quarkus.flyway.sql-migration-prefix=V
 quarkus.flyway.migrate-at-start=true
 quarkus.flyway.placeholders.foo=bar
diff --git a/integration-tests/flyway/src/main/resources/db/location4/V1.0.2__Quarkus.sql b/integration-tests/flyway/src/main/resources/db/location4/V1.0.2__Quarkus.sql
new file mode 100644
index 0000000000000..b678109e4662c
--- /dev/null
+++ b/integration-tests/flyway/src/main/resources/db/location4/V1.0.2__Quarkus.sql
@@ -0,0 +1,2 @@
+INSERT INTO TEST_SCHEMA.quarkus_table2(id, name)
+VALUES (2, '1.0.2 QUARKED');
diff --git a/integration-tests/flyway/src/test/java/io/quarkus/it/flyway/FlywayFunctionalityTest.java b/integration-tests/flyway/src/test/java/io/quarkus/it/flyway/FlywayFunctionalityTest.java
index 306e67bf1bbe1..1002515d3b09b 100644
--- a/integration-tests/flyway/src/test/java/io/quarkus/it/flyway/FlywayFunctionalityTest.java
+++ b/integration-tests/flyway/src/test/java/io/quarkus/it/flyway/FlywayFunctionalityTest.java
@@ -15,7 +15,7 @@ public class FlywayFunctionalityTest {
     @Test
     @DisplayName("Migrates a schema correctly using integrated instance")
     public void testFlywayQuarkusFunctionality() {
-        when().get("/flyway/migrate").then().body(is("1.0.1"));
+        when().get("/flyway/migrate").then().body(is("1.0.2"));
     }
 
     @Test