While microwave radiation does penetrate the surface of food and start to heat the inside at roughly the same time as the surface, it's not necessarily accurate to say the food is cooked from the inside out. Microwaves heat food by being absorbed primarily by liquid water molecules, and to a lesser extent fats and some sugars, imparting energy to them in the form of heat.

Contrary to what many think, the frequency at which microwave ovens operate, 2.45 GHz, is not tuned to the maximum absorption frequency of water. That frequency is actually closer to 10 GHz, and if ovens operated there, food would be heated even less inside, since the bulk of the radiation would be absorbed at or near the surface due to the short wavelength.

If a food is of uniform consistency and high in water content, most of the microwave energy will be absorbed by the water near the surface before it gets into the center of the food, and the food will heat from the outside in, as with traditional ovens. On the other hand, if the surface of the food is drier than the center, as with bread or a baked potato, the center will heat up faster. You can see this clearly if you microwave foods with a dry outer crust and a moist filling, like a McDonald's apple pie. If you cook it for about 20 seconds in a typical oven, you'll find that the crust is fairly cool to warm, while the filling can be quite hot.

Because of this characteristic of microwaves, the microwave cooking instructions for many foods specify a "stand time"--after you remove the food from the microwave, you're supposed to let it stand for a prescribed time before serving. This lets the heat diffuse through the food via ordinary conduction so that a uniform temperature is reached. In fact, some foods, especially large items such as a meatloaf, are best cooked in cycles: Heat for a few minutes, allow to stand for a while, then repeat. Most microwave ovens do just that when you put them on a lower power setting. Instead of actually lowering the power, the oven cycles the magnetron on and off to achieve the desired power on average. In other words, if you set the oven to run at 50% power, it will turn the magnetron on for, say, 30 seconds, then off for 30 seconds, then on, and so on. This keeps the outside from overcooking while allowing the inside to be cooked thoroughly.