Microwaves are part of the natural world, and were not invented by people. Microwave devices use that part of the spectrum in ways not common to living creatures on Earth, but all living things on Earth have always been living in an environment that included microwave radiation.
No other living things have used fire as humans do either. It is not factual to claim that somehow fire is natural and microwaves aren't. Both are being used by humans in novel ways to cook.