There is a big debate going on about whether soy or milk is better for you. This debate has spewed over into protein powders: Is it better to supplement with whey (from milk) protein or soy protein?
Whey protein may help to support the immune system. An improved immune system keeps you from getting sick and helps your training goals.
Whey protein has factors that in the body translate into growth hormone derivatives. This can help in muscle recovery and overall performance.
Whey protein gets into the blood stream and the muscles fast. This is great for after a workout--it helps to jump-start recovery and give the muscles much needed amino-acids for growth.
Whey protein is often pasteurized, which can damage some of the proteins and growth factors, rendering them useless to the body.
Whey protein may be filled with estrogenic chemicals used in the cattle industry to cause weight gain.
Whey protein may cause lactose intolerance issues--when you're lactose intolerant, you don't have the enzyme needed to break down the lactose sugar. This can cause bloating, gas and other intestinal issues. Some proteins have the lactose removed to deal with this problem.
Soy protein has no lactose sugar. This means that people who are lactose intolerant can drink it without fear of intestinal disturbances.
Soy protein powder is completely plant derived. This is preferred for vegans who avoid the use of all animal products.
Soy is one of the only plant-based sources of complete proteins. Most plants do not have all of the amino acids required by the body, but soy does.
Soy Protein is pasteurized, causing it to lose much of its nutritional value. It also has protein-inhibitors that prevent your body from being able to use the protein fully.
The fiber in soy protein can be harsh and tough. This is bad for people with a sensitive digestive tract.
Soy contains phytates, which may inhibit mineral digestion and even iodine absorption. This can potentially cause a loss in bone density, leading to weaker bones or decreased thyroid function, causing weight gain and a lowered metabolism.
Soy contains isoflavones that have the potential to increase your estrogen levels. Excess estrogen for men or women can cause increased weight gain and exacerbate other estrogen-related issues.
Much of the soy today is "bathed in a toxic, explosive chemical solvent known as hexane." Hexane may cause a number of health complications and also is not good for the environment (Resources).
Both whey and soy have their pros and cons. But it appears problems associated with soy protein are much worse than those associated with whey protein. Between the two, a high quality whey protein would be the best choice.