diff --git a/contribs/application/src/main/java/org/matsim/application/MATSimApplication.java b/contribs/application/src/main/java/org/matsim/application/MATSimApplication.java
index 6a3b0ef9e04..34bef66a51c 100644
--- a/contribs/application/src/main/java/org/matsim/application/MATSimApplication.java
+++ b/contribs/application/src/main/java/org/matsim/application/MATSimApplication.java
@@ -341,7 +341,8 @@ public static void run(Class<? extends MATSimApplication> clazz, String... args)
 			// Pass stored args to the instance as well
 			if (System.getenv().containsKey("MATSIM_GUI_ARGS")) {
 				String[] guiArgs = System.getenv("MATSIM_GUI_ARGS").split(ARGS_DELIMITER);
-				args = ApplicationUtils.mergeArgs(args, guiArgs);
+				if (guiArgs.length > 0)
+					args = ApplicationUtils.mergeArgs(args, guiArgs);
 			}
 		}
 
@@ -376,9 +377,12 @@ public static void runWithDefaults(Class<? extends MATSimApplication> clazz, Str
 
 		if (ApplicationUtils.isRunFromDesktop()) {
 
-			String value = String.join(ARGS_DELIMITER, defaultArgs);
-			System.getenv().put("MATSIM_GUI_ARGS", value);
+			if (defaultArgs.length > 0) {
+				String value = String.join(ARGS_DELIMITER, defaultArgs);
+				System.setProperty("MATSIM_GUI_ARGS", value);
+			}
 
+			// args should be empty when run from desktop and is not used
 			run(clazz, "gui");
 
 		} else {
diff --git a/matsim/src/main/java/org/matsim/run/gui/ExeRunner.java b/matsim/src/main/java/org/matsim/run/gui/ExeRunner.java
index 7c1b75eac56..fac8a5df38d 100644
--- a/matsim/src/main/java/org/matsim/run/gui/ExeRunner.java
+++ b/matsim/src/main/java/org/matsim/run/gui/ExeRunner.java
@@ -100,8 +100,8 @@ public void run()  {
 
 			// Copy the MATSIM_GUI_ARGS environment variable to the process environment
 			// these arguments may be used internally by the matsim scenario
-			if (System.getenv().containsKey("MATSIM_GUI_ARGS")) {
-				processBuilder.environment().put("MATSIM_GUI_ARGS", System.getenv("MATSIM_GUI_ARGS"));
+			if (System.getProperty("MATSIM_GUI_ARGS") != null) {
+				processBuilder.environment().put("MATSIM_GUI_ARGS", System.getProperty("MATSIM_GUI_ARGS"));
 			}
 
 			if (workingDirectory != null) {