It is easy to see why people would think that cooking food in the microwave kills all the bacteria. It comes from the misconception that microwaving ‘irradiates’ food and so destroys any bacteria, along with all the nutrients.
It is not true at all. The fact is, as you can learn from this article about microwaves cooking food from the inside out, it is heat that cooks your food in the microwave. If the food doesn’t get hot enough to kill all the bacteria, contaminated chicken, meat, or any other food could still make you sick.
There is a reason why microwavable meals stress that the product should be heated up to a certain internal temperature, usually around 165 F. For more, see safe food temperatures.
If you heat food up long enough in the microwave, it will sterilize the food, but the same can be said of any sufficient heat source. The microwave radiation, however, is not ionizing radiation, and it does not make food radioactive. You can also sterilize a kitchen sponge in the microwave, but this is no different from boiling the sponge in water for a few minutes.
To be clear, when foods are actually exposed to ionizing radiation to kill microorganisms, insects, and etc. the food’s chemistry is altered, so-called radiolytic products (RP’s), caused by radiation striking the molecules and causing them to lose electrons and form free radicals. Most of these RP’s are found naturally in non-radiated foods, so they are not thought to pose any hazard.
When unique radiolytic products are formed (URP’s), there is more concern about human safety.
Microwaving, however, does not produce any RP’s at all. There is more cause for concern in regards to microwave food packaging than there is for the microwave’s effect on the food itself, as it is possible for materials in the packaging to migrate into the food at very high temperatures.
As for heating up foods in your own containers, the safest materials to use in the microwave are microwave-safe ceramics or glass.
For nutrients, it is a bit more complicated.
First, when people say nutrients, they mean micronutrients, but proteins, fats, and carbohydrates, are also nutrients, called macronutrients. Some micronutrients can be lost through cooking, and the amount and type of nutrients lost depend on the cooking method and temperatures reached.
Although it may be possible for more nutrient retention in microwaving due to shorter cooking times, in general, it’s a wash: Microwaving should not be expected to cause any more nutrient loss than other cooking methods, nor should it generally be expected to retain more nutrients. Proteins become denatured through cooking, but this doesn’t not affect the ability of the body to use them. There is some evidence that vegetables blanched in the microwave may retain more vitamin C, and that there may be greater retention b vitamins such as thiamine in meat products, but the evidence is inconsistent. Don’t count on it making a huge difference in your overall nutrition.