diff --git a/src/main/java/org/scijava/launcher/Java.java b/src/main/java/org/scijava/launcher/Java.java
index 8705679..dc9b299 100644
--- a/src/main/java/org/scijava/launcher/Java.java
+++ b/src/main/java/org/scijava/launcher/Java.java
@@ -325,6 +325,19 @@ public static void upgrade(BiConsumer<String, Double> subscriber)
 			String configFileValue = System.getProperty("scijava.app.config-file");
 			if (configFileValue != null && !configFileValue.isEmpty()) {
 				File configFile = new File(configFileValue);
+				String appDirValue = System.getProperty("scijava.app.directory");
+				if (appDirValue != null) {
+					Path appDirPath = Paths.get(appDirValue).normalize().toAbsolutePath();
+					// If possible, use a path relative to the application directory.
+					// This improves portability if the application gets moved
+					// elsewhere, and/or accessed from multiple operating systems.
+					try {
+						newJavaPath = appDirPath.relativize(newJavaPath);
+					}
+					catch (IllegalArgumentException exc) {
+						Log.debug(exc);
+					}
+				}
 				Config.update(configFile, "jvm.dir", newJavaPath.toString());
 			}
 		}