Of your influence on food the most important is choice. The next is how you cook it.
Heating helps break down food structure so nutrients are more available. In moderate cooking, few nutrients are lost and those that remain are more easily assimilated.
Excessive heat damages nutrients in food. Vitamins are extremely sensitive to heat and minerals can be drawn out of food when cooked in water.
Steaming vegetables is the best way to cook them. This way you retain micronutrients and yet make the vegetables more digestible. Fruits are best eaten raw, retaining all nutrients.
Microwaving is never a good idea. A prestigious medical journal reports that microwave cooking alters food enough to cause, upon ingestion, “structural, functional and immunological changes” in the body. It further says that the microwave transforms the amino acid L-Proline into D-Proline, a proven toxin to the nervous system, liver and kidneys.