According to Recipe Tips, eating raw sprouts is not recommended because of the risk of bacteria and food illness. Cooking alfalfa sprouts will kill any potential bacteria on them, ensuring safety. Sprouts only stay fresh for a few days, even if you keep them in the refrigerator. Buy only as much as you can eat in a couple of days and discard when the sprouts become slimy or wilted.
Add alfalfa sprouts to stir-fries, but wait until the last minute. According to Recipe Tips, sprouts shouldn't be cooked for more than 30 seconds, or they'll become wilted. Saute all vegetables you plan on cooking, then add sprouts for a quick mix at the end.
Add alfalfa sprouts to soups and stews. Wait until the soup has finished cooking, then mix in the alfalfa sprouts. The heat of the water will slightly cook the sprouts without completely eliminating their crunchy texture.
Place the alfalfa sprouts in a tray and place them in the oven for a minute or two. This will "toast" the sprouts, giving them a crispy texture while cooking them and getting rid of any bacteria that might be present. Take them out before they turn brown. Add them to salads, sandwiches or wraps.