Step 1: After soaking the black beans overnight, drain and place them in a large pot with the garlic, thyme, and oregano. Cover with water and bring to a boil, reduce to simmer. Reduce the heat to low and simmer until the beans are very tender, about 3 hours. Add water is needed to keep the beans submerged throughout cooking. Remove the garlic, thyme, and oregano sprigs. Drain the beans, reserving 2/3 cup of the cooking liquid.
Step 2: Place the lard or butter in a large saute pan and heat until shimmering (if using butter, be careful not to burn it). Carefully transfer the beans and their reserved liquid to the pan. With a potato masher or a large fork, smash the beans to the degree you desire. Stir in the honey, chipotles, and 1 1/4 teaspoons of the salt. The beans can be prepared to this point 2 or 3 days in advance and refrigerated. Reheat over medium-low heat, adding water if necessary to loosen the beans.
Step 3: Place the shallots in a 9-inch saute pan. Cover with oil and place over medium-high heat. Watch carefully and stir constantly once the oil heats up. Reduce the heat to medium and cook the shallots until they are golden brown, about 5 minutes. Use a slotted spoon to remove them to drain on a paper towel. Season the shallots with the remaining 1/8 teaspoon salt. Place the beans in a serving bowl and top with queso fresco (or cheddar), fried shallots, and cilantro sprigs.
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