Lay the dried black beans on a baking sheet and pick out any stones or broken pieces. Transfer the beans to a Dutch oven or heavy stockpot and add enough water to cover them by about 2 inches. Let the beans soak for at least 4 hours or up to overnight. Once soaked, drain the beans and set them aside.
Place the Dutch oven on medium heat and allow it to warm up. Once hot, add the olive oil, followed by the diced onion and jalapeño (if using). Stir occasionally and cook until the onion softens, about 5 to 7 minutes. Add the minced garlic and sauté for another minute until fragrant.
Stir in the chili powder, ground cumin, and dried oregano, mixing well until the spices are fragrant, about 1 minute. Add the drained beans, chipotles in adobo (if using), and 6 cups of water. Bring the mixture to a simmer, cover the pot partially, and let it cook for 1 ¼ to 2 hours. Stir occasionally and check the beans for tenderness as they cook.
Once the beans are tender, stir in the lime juice and season with 1 teaspoon of kosher salt. Taste the beans and adjust the seasoning by adding more salt if necessary.
Transfer the cooked beans to an airtight container and refrigerate them. They can be stored for up to 1 week and reheated as needed.