Best Answer: No, it's not going to hurt you, more than likely. Rust comes from moisture protecting an iron metal surface (oxidizing it, forming iron oxide, which is rust). Unless your rust extensive, it won't hurt the microwave's operation.However, the rust could lead to a penetration of the metal and thus electric arcing when the oven is operating -- that's very bad. Arcing could make the spot larger or even cause microwave energy to leak. You can touch it up, if it isn't too bad.owever, the rust could lead to a penetration of the metal and thus electric arcing when the oven is operating -- that's very bad. Arcing could make the spot larger or even cause microwave energy to leak. You can touch it up, if it isn't too bad.