Cooking food may destroy enzymes and the chemicals which plants produce in order to try to prevent them being palatable to animals. This may improve the flavour, texture and digestibility of the raw food.
Cooking foods in liquid and then throwing away the liquid is very wasteful of many nutrients, particularly the water soluble vitamins such as thiamin, riboflavin, niacin and vitamin C. There is almost never any need to discard cooking water if the right amount is used in the first place. Any surplus liquid should be used for soups and gravies, or even, as in China, served as a cold drink.
The most nutrients are lost at high temperatures and by prolonged cooking. Foods left to stand may also lose nutrients.
Microwave and infra-red cooking can improve the nutritional status of food by reducing the use of liquids and cooking times. They are a good way of reheating food, provided the food is heated right through.
Cooking protein and starches together results in destruction of the amino acid lysine, severely degrading the quality of the protein. Prolonged cooking of protein can also make it more difficult to digest.