I am not talking about magically or spiritually, as High Priestess Lydia Coventina already said. I recommend cooking everything on a pan on the stove over a gas flame.
But there is no health problems from a microwave itself. As long as you are using a glass or ceramic container that is safe for high temperature, and never use platic or metal in a microwave. It is not radiation like an xray or anything like that. It is just a magnetic field from AC voltage, so for 60Hz or 50Hz frequency AC main line voltage, the direction of the magnetic field reverses twice in every cycle. Water is a polar molecule with a magnetic north and south pole sides to it. So when the magnetic field switches directions 120 or 100 times every second, every water molecule physically rotates to align with it. And the friction from the water molecules rotating is what heats it up.