It turns out that an alkaline environment starts a chemical reaction that causes the cell structure of legumes to break down. When we add baking soda to a pot of cooking beans, it results in tender beans in less time.
On the flip side, adding acid causes the cell structure of legumes to remain firm. If there is too much acid in the pot, the beans may never soften enough to be ready to eat. This means that you should be careful when cooking beans with acidic ingredients, especially tomatoes, citrus juices, and vinegar. We find it is best to add citrus juices and vinegars at the end of the cooking process—when the beans are already softened. (This also preserves the flavor of these acidic ingredients.) Tomatoes generally need some cooking time, so we often add tomatoes (including all canned tomato products) partway through the cooking process, after the beans have softened considerably.
The lesson? Along with brining and soaking, baking soda can work wonders on beans, saving you up to an hour of cooking time. Just be sure not to add more than a pinch—too much and the beans can end up tasting soapy and unpleasant.