Sort through the dry pinto beans using a large colander, removing any small stones or damaged beans. Rinse thoroughly under cool water, then transfer to a large bowl. Cover the beans with 2 to 3 inches of water, skimming off and discarding any that float. Let the beans soak at room temperature for at least 8 hours, or overnight for best results. Once soaked, drain and rinse them well.
Heat a large pot or Dutch oven over medium heat and add the avocado oil. Once shimmering, add the chopped onion and sauté until soft and translucent, about 5 minutes. If you prefer a bit of heat, add the diced jalapeño alongside the onion and cook until softened.
Stir in the ground cumin, allowing the spice to toast briefly and release its aroma. Add the soaked pinto beans, fresh water, oregano, sea salt, and several cracks of black pepper. Bring the mixture to a rolling boil, then reduce the heat to maintain a steady simmer. Cook uncovered until the beans are tender and creamy. Begin checking at the 1-hour mark, then every 15 minutes afterward. Depending on the age of the beans, total cooking time may vary. Add more water as needed to ensure the beans remain fully submerged during cooking.
Once the beans are tender and the liquid has thickened to your liking—almost stew-like in consistency—remove the pot from the heat. Stir in the fresh lime juice, and taste for seasoning. Add more salt, pepper, and chili powder if desired. Garnish with chopped fresh cilantro for a final pop of flavor.
Store any leftovers in an airtight container in the refrigerator for up to 5 days, or freeze for longer storage, up to 3 months.