Beanno. Buy a large bottle.

Many methods exist to degas beans but they appear to be mostly myth. Making sure the beans are well cooked seems to be most effective. Maybe a pressure cooker would help.

Seriously, buy Beanno!

I was going to say discard the water after soaking or boiling, but you already do that. A lot of how you personally handle beans has to do with how often you eat them. The more often/consistently you put them in your system, the more enzymes you produce to digest them without upset. But why you might have a problem with homemade beans, and not with the Whole Foods soup, I don't know and will be interested to see if anyone can share an insight or knowledge to explain.

Putting a teaspoon or two of baking soda in the soak water will cut the gas producing tendencies quite a lot. Just be sure to rinse really well before cooking, so you don't have the flavor of the baking soda in your finished product. This method doesn't seem to be 'mostly myth', as it has really worked for us.
Rusty

I must be sensitive, the baking soda didn't make any difference in my world. Or vinegar. Or fennel seed. Or tossing the soak water. I simply avoid anything bean-y. Bummer, cuz I likes 'em!

But eating slightly undercooked beans was a terrible experience!

Barnmom -- I get what you're saying about just avoiding them, but am still perplexed about the Whole Foods beans. We're going over there right now and I'll ask them what they do, and report back. Thanks for the thought but anything like Beano is completely out of the question for me. I would skip the beans before taking something for it.

Rusty, I didn't know about the baking soda and will try it, thanks.

Rhome -- hmmm, that's interesting, so we have to eat beans a lot and get used to them. That explains a lot!

Here is their recipe:

Chipotle Black Bean Soup

Serves 6 to 8

The smoky, spicy almost chocolate-like flavor of this soup comes from chipotle chiles, an ingredient that is very popular in the Southwest. Chipotle chiles, which are smoked jalape¤os, can be found dried, pickled or canned in thick adobo sauce. This recipe calls for unsweetened cocoa, which adds a warmth to the complex flavor of this soup. Enjoy it with corn bread to buffer the chiles. From The Whole Foods Market Cookbook

Ingredients

2 tablespoons olive oil
2 cups chopped red onion
1 medium red bell pepper, seeded and chopped
1 medium green bell pepper, seeded and chopped
2 cloves garlic, minced
1 tablespoon dried oregano, or 3 tablespoons fresh
1 tablespoon ground cumin
3 chopped canned chipotle chiles
1/8 cup adobo sauce from canned chipotle peppers
12 cups water
1 bay leaf
2 cups (dry) black beans, rinsed
1 tablespoon unsweetened cocoa powder
3/4 cup orange juice
1/2 cup minced fresh cilantro
6 scallions, thinly sliced
Sea salt

Method

Soak the black beans overnight or 6 to 8 hours prior to cooking.

Heat the olive oil in a large pot over medium-high heat. Add the red onion, peppers and garlic; saut until the onion is translucent. Reduce the heat to medium-low, and add the oregano, cumin, chipotle chiles, and adobo sauce; saut for 1 minute. Add the cold water, bay leaf, and beans. Bring the soup to a boil, then lower to a simmer and cook uncovered for 1 1/2 to 2 hours, until the beans are tender.Stir in the cocoa powder, orange juice, cilantro, scallions, and salt; continue to simmer for 5 minutes.

Nutrition

Per serving (about 22oz/612g-wt.): 290 calories (50 from fat), 6g total fat, 1g saturated fat, 0mg cholesterol, 950mg sodium, 48g total carbohydrate (8g dietary fiber, 11g sugar), 13g protein

Maybe it's the orange juice?

Here is a link that might be useful: Whole Foods black bean soup recipe

The gas you produce after eating beans comes from undigested bits of certain proteins and carbohydrates. Baking soda, fennel or anything else won't help a bit. The secret is to make sure your beans are well cooked, and if you haven't eaten beans in a while, don't "pig out"...eat a small polite serving and gradually work up to "pig out".
And as has been suggested...Beano...it supplied the enzyme to digest the beans which you are missing.
And black beans are among the worst in terms of bits that are hard to digest.
Most likely the reason why the canned ones don't bother you is because they have been well cooked....AND they were fresh when processed. Beans that have been stored a while become hard and take a lot longer to cook.
Linda c

yes you can certainly train your body to not react so badly to beans by eating more...I have found that actually doing the 3 boil helps too..soak over night or not...bring to a boil, turn off, let sit 20 minutes or so, drain, refill pan, bring to a boil, do it all 3 times...then final drain and then cook the beans as you like...
It does help...but it's a process...

Some times, certain beans have more issues with intesines than others too...and certainly cooking them down to "mush" as in refried..helps too...

I think it's not just eating more beans but eating more fiber in general - beans included. If you have a healthy diet with different kinds of fiber and ruffage (sp?) everyday, then eating beans shouldn't be a surprise to your intestines. That said, age has something to do with it , I think. Seems like the older people get the more problems they have with that particular problem. I agree that black beans cause more wind than other beans. I've known several people who avoid them. Including my husband who refuses to eat them on a week night, lol. And he gets lots of fiber and ruffage daily.

Someone else on the CF mentioned boiling rapidly during the cooking process would do it. But, they didn't say at which point in the process.

I recently ordered some dried epazote and I tried some in red beans. That's supposed to help but I can't attest to that as I don't normally have that problem. I bought it with black beans in mind. :)

Well thank you everybody, lots of good ideas here, which I will try.

We just got back from Whole Foods, and the cook there (though not the main chef, they're a little short staffed today) said, and I kid you not, that they just bring the water to a boil and dump everything in at once including the dried (I repeat DRIED, not pre-cooked) beans, and let it cook for about 30-45 minutes. No pre-soaking whatsoever. I'm going to call back and ask the actual chef, because this doesn't agree with what they say online. Thanks Barnmom, it sounds more delicious than the recipe they have in this store, which is missing some of those ingredients like chocolate, orange juice and scallions.

Linda and Terri I think what you say is right, about making sure they are done and pulverized, because I make refried beans from Bush's canned pinto beans and there's no problem. It's only when I make things from dried, and I have always been so mystified when (even with split peas) they would stay hard no matter how long I cooked them. Now I know -- they just get old. Makes perfect sense.

I'm thinking of just getting some canned black beans and making soup with them!

Thanks all.

I almost always just dump the beans into a pot....no soaking or anything...