Methods and systems for safe execution of guest code in virtual machine context are presented. A method for running a virtual machine in a computing system includes (a) launching a virtual machine monitor (VMM) that uses a software debugger; (b) launching a virtual machine (VM) that can natively run safe instructions; (c) determining, at runtime, if the instruction is safe or potentially unsafe; (d) executing safe instructions in a native mode; and (e) activating control logic to process potentially unsafe instructions in the software debugger. The software debugger can bypass at least one of the potentially unsafe instructions. The potentially unsafe instructions include instructions that cannot be safely executed in the context of the VM, and instructions that can cause unpredictable results in the context of the VM.