In MobaXterm 11.1 and 12.1, the protocol handler is vulnerable to command injection. A crafted link can trigger a popup asking whether the user wants to run MobaXterm to handle the link. If accepted, another popup appears asking for further confirmation. If this is also accepted, command execution is achieved, as demonstrated by the MobaXterm://`calc` URI.

In MobaXterm 11.1, the mobaxterm: URI handler has an argument injection vulnerability that allows remote attackers to execute arbitrary commands when the user visits a specially crafted URL. Based on the available command-line arguments of the software, one can simply inject -exec to execute arbitrary commands. The additional arguments -hideterm and -exitwhendone in the payload make the attack less visible.

In MobaTek MobaXterm Personal Edition v11.1 Build 3860, the SSH private key and its password can be retrieved from process memory for the lifetime of the process, even after the user disconnects from the remote SSH server. This affects Passwordless Authentication that has a Password Protected SSH Private Key.