Energy-autonomous computing devices have the potential to extend the reach of computing to a scale beyond either wired or battery-powered systems. However, these devices pose a unique set of challenges to application developers who lack both hardware and software support tools. Energy harvesting devices experience power intermittence which causes the system to reset and power-cycle unpredictably, tens to hundreds of times per second. This can result in code execution errors that are not possible in continuously-powered systems and cannot be diagnosed with conventional debugging tools such as JTAG and/or oscilloscopes. We propose the Energy-interference-free Debugger, a hardware and software platform for monitoring and debugging intermittent systems without adversely effecting their energy state. The Energy-interference-free Debugger re-creates a familiar debugging environment for intermittent software and augments it with debugging primitives for effective diagnosis of intermittence bugs. Our evaluation of the Energy-interference-free Debugger quantifies its energy-interference-freedom and shows its value in a set of debugging tasks in complex test programs and several real applications, including RFID code and a machine-learning-based activity recognition system.