diff --git a/build-tools-internal/src/main/java/org/elasticsearch/gradle/internal/TestFixtureApplicationConsumerPlugin.java b/build-tools-internal/src/main/java/org/elasticsearch/gradle/internal/TestFixtureApplicationConsumerPlugin.java
index 041b11b6a6092..6528092760b19 100644
--- a/build-tools-internal/src/main/java/org/elasticsearch/gradle/internal/TestFixtureApplicationConsumerPlugin.java
+++ b/build-tools-internal/src/main/java/org/elasticsearch/gradle/internal/TestFixtureApplicationConsumerPlugin.java
@@ -51,7 +51,7 @@ public void apply(Project project) {
                     Collection<String> services = fixtureApps.getFixtureApplications().get(appKey);
                     if (services.isEmpty() == false) {
                         String appHomeKey = "fixture." + appKey + ".home";
-                        applySysProps.accept(appHomeKey, file.getAbsolutePath());
+                        applySysProps.accept(appHomeKey, test.getWorkingDir().toPath().relativize(file.toPath()).toString());
                         AtomicInteger index = new AtomicInteger();
                         services.forEach(
                             (serviceName) -> applySysProps.accept("fixture." + appKey + ".service." + index.getAndIncrement(), serviceName)