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 4e4c6860d63..2425a0f1491 100644
--- a/contribs/application/src/main/java/org/matsim/application/MATSimApplication.java
+++ b/contribs/application/src/main/java/org/matsim/application/MATSimApplication.java
@@ -413,6 +413,8 @@ public static void runWithDefaults(Class<? extends MATSimApplication> clazz, Str
 
 		if (ApplicationUtils.isRunFromDesktop() && args.length == 0) {
 
+			System.setProperty("MATSIM_GUI_DESKTOP", "true");
+
 			if (defaultArgs.length > 0) {
 				String value = String.join(ARGS_DELIMITER, defaultArgs);
 				System.setProperty("MATSIM_GUI_ARGS", value);
diff --git a/contribs/application/src/main/java/org/matsim/application/ShowGUI.java b/contribs/application/src/main/java/org/matsim/application/ShowGUI.java
index e394bfd7b79..6400262eb95 100644
--- a/contribs/application/src/main/java/org/matsim/application/ShowGUI.java
+++ b/contribs/application/src/main/java/org/matsim/application/ShowGUI.java
@@ -40,6 +40,13 @@ public Integer call() throws Exception {
 
         Gui gui = f.get();
 
+		// Set the current working directory to be used in the gui, when run from the command line
+		// If the gui is run from desktop, the working directory is not overwritten
+
+		// Assumption is that starting something from command line, the user expects that the working directory remains the same
+		if (!System.getProperty("MATSIM_GUI_DESKTOP", "false").equals("true"))
+			gui.setWorkingDirectory(new File(""));
+
         while (gui.isShowing())
             Thread.sleep(250);
 
diff --git a/matsim/src/main/java/org/matsim/run/gui/Gui.java b/matsim/src/main/java/org/matsim/run/gui/Gui.java
index 4b826b14842..1ca4a9afc8d 100644
--- a/matsim/src/main/java/org/matsim/run/gui/Gui.java
+++ b/matsim/src/main/java/org/matsim/run/gui/Gui.java
@@ -91,6 +91,11 @@ public class Gui extends JFrame {
 
 	private File configFile;
 	private File lastUsedDirectory;
+
+	/**
+	 * This is the working directory for the simulation. If it is null, the working directory is the directory of the config file.
+	 */
+	private File workingDirectory = null;
 	private ConfigEditor editor = null;
 	private ScheduleValidatorWindow transitValidator = null;
 
@@ -439,6 +444,8 @@ private void startMATSim() {
 		textStdOut.setText("");
 		textErrOut.setText("");
 
+		String cwd = workingDirectory == null ? new File(txtConfigfilename.getText()).getParent() : workingDirectory.getAbsolutePath();
+
 		new Thread(() -> {
 			String classpath = System.getProperty("java.class.path");
 			String[] cpParts = classpath.split(File.pathSeparator);
@@ -457,8 +464,7 @@ private void startMATSim() {
 					"--add-exports", "java.desktop/sun.java2d=ALL-UNNAMED",
 					mainClass, txtConfigfilename.getText() };
 			// see https://jogamp.org/bugzilla/show_bug.cgi?id=1317#c21 and/or https://github.com/matsim-org/matsim-libs/pull/2940
-			exeRunner = ExeRunner.run(cmdArgs, textStdOut, textErrOut,
-					new File(txtConfigfilename.getText()).getParent());
+			exeRunner = ExeRunner.run(cmdArgs, textStdOut, textErrOut, cwd);
 			int exitcode = exeRunner.waitForFinish();
 			exeRunner = null;
 
@@ -575,6 +581,10 @@ public static void main(String[] args) {
 		Gui.show("MATSim", RunMatsim.class, args.length == 1 ? new File(args[0]) : null);
 	}
 
+	public void setWorkingDirectory(File cwd) {
+		this.workingDirectory = cwd;
+	}
+
 	// Is it a problem to make the following available to the outside?  If so, why?  Would it
 	// be better to rather copy/paste the above code and start from there?  kai, jun/aug'18