But unfortunately, that's not the end of the story for soy and gluten.
Soybeans commonly are grown in rotation with wheat crops. That means the farmers use the same fields to grow soy and wheat, along with the same combines to harvest them, the same storage facilities to keep them and the same trucks to transport them to market. As a result, soy can be subject to gluten cross-contamination in some cases, lots of gluten cross-contamination.
For example, a 2010 study by celiac dietitian Tricia Thompson on gluten in so-called 'gluten-free' grains found that soy was one of the worst offenders in fact, one sample of soy flour contained a whopping 2,925 parts per million of gluten (for comparison, less than 20 parts per million generally is considered "gluten-free," although many people react to even less gluten than that).
Scary, isn't it?
In my experience, soy is one of the most cross-contaminated of all crops right up there with oats, which also are grown in rotation with gluten crops.
Many people report reacting to soy in a similar fashion as they do to wheat and other gluten grains. Now, soy is a pretty allergenic food it's one of the top eight allergens in the U.S. Still, I suspect that one reason so many celiacs and gluten-sensitive people report "soy intolerances" (not true allergies) is due to high levels of gluten cross-contamination in the soy ... not due to a problem with the soy itself.
If you think this might be the case with you, you'll probably have your best luck looking for soy products that are certified gluten-free. Gluten-free certification programs require food manufacturers to follow strict sourcing guidelines for their raw materials, which means the end products will contain less cross contamination, too in fact, all three gluten-free certification programs in the U.S. require products to test at less than at least 10 parts per million of gluten.
If you want soy flour or soy protein to use in baking or for other cooking projects, both Bob's Red Mill and Arrowhead Mills have gluten-free-labeled soy products that contain less than 20 parts per million of gluten.
Meanwhile, if you want soy sauce (remember, most conventional soy sauce products include wheat as a major ingredient), take a look at my list of gluten-free soy sauce options, some of which are certified gluten-free.