diff --git a/tools/cooja/java/org/contikios/cooja/Cooja.java b/tools/cooja/java/org/contikios/cooja/Cooja.java
index 055cb46f4..d053fd45e 100644
--- a/tools/cooja/java/org/contikios/cooja/Cooja.java
+++ b/tools/cooja/java/org/contikios/cooja/Cooja.java
@@ -3152,7 +3152,7 @@ public class Cooja extends Observable {
         if (new File(logConfigFile).exists()) {
           DOMConfigurator.configure(logConfigFile);
         } else {
-          System.err.println("Failed to open " + logConfigFile);
+          logger.error("Failed to open " + logConfigFile);
           System.exit(1);
         }
       } else if (new File(LOG_CONFIG_FILE).exists()) {
diff --git a/tools/cooja/java/org/contikios/cooja/dialogs/SerialUI.java b/tools/cooja/java/org/contikios/cooja/dialogs/SerialUI.java
index bcc1a0734..430939482 100644
--- a/tools/cooja/java/org/contikios/cooja/dialogs/SerialUI.java
+++ b/tools/cooja/java/org/contikios/cooja/dialogs/SerialUI.java
@@ -165,8 +165,7 @@ public abstract class SerialUI extends Log implements SerialPort {
             writeString(command);
           }
         } catch (Exception ex) {
-          System.err.println("could not send '" + command + "':");
-          ex.printStackTrace();
+          logger.error("could not send '" + command + "':", ex);
           JOptionPane.showMessageDialog(
               logTextPane,
               "Could not send '" + command + "':\n" + ex.getMessage(), "Error sending message",