According to Harvard Health Publications, certain nutrients, such as vitamin C, will break down when exposed to heat, regardless of whether you cook using a microwave or through more conventional methods. However, because microwaves cook foods quicker, they may actually do a better job of preserving nutritional content that can be destroyed as a result of high heat exposure. Nutrients are also better preserved when minimal amounts of water are used during cooking. To further preserve the nutritional content of vegetables, Columbia University recommends not peeling the vegetables and using large pieces. Cover the foods so they steam during the cooking process, further reducing the cooking time.