The night before you are cooking your beans, sift through the pintos beans to make sure there are no small pebbles. (Yes, this is a thing.) Rinse them with water and then put them in a bowl giving them plenty of space to expand. Cover with a plate or plastic wrap and put in the fridge to soak.
The next day, drain and rinse the beans. These should expand to roughly double the size, giving you 4 cups of beans.
In a large heavy bottom pot, heat the 2 tablespoons of olive oil over medium-high heat. Be sure that this pot is large enough to let those beans expand yet again. When the oil is hot, add in the onion and saute for 4-6 minutes until opaque.
Gently add the soaked beans, the fresh thyme, the bay leaf, the garlic, the peppers/chilies, the bouillon, and the water. Add 1 ½ teaspoons of salt. The water should cover the beans by at least an inch in the pot you end up using. If you need to add more or have less, add or get rid of accordingly.
Bring everything to a boil on high heat. As soon as you get a good bubble, bring that heat back down to a simmer. Skim the top of the liquid of any scum that has formed. The more of this you can get rid of the better, but don’t drive yourself crazy. Once you are happy, add a healthy glug (or three of olive oil or a heaping spoon of lard.) Keep an eye on the beans and stir every 15-20 minutes or so.
About an hour into the process, taste a bean. It should be easy to bite into and starting to take on flavor. Add another teaspoon of salt here.
At the 90 minute mark, do another quick taste test. Add more salt if needed and see how cook the beans are. Keep checking a bean every 15 minutes or so until they are done. They should be creamy and tender.
When you reach that point you can serve them in their broth or drain them and serve them on their own with your favorite protein.
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Notes
You can use vegetable broth or stock for vegetarian beans.This recipe can be used for any dry beans.