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Step 1
Place chicken in a large pot and cover with cold water. Bring to a boil, turn off the heat, cover the pot and let sit for 25 minutes. Transfer chicken to a large bowl or a colander placed in the sink to cool. Return the pot with the cooking liquid to the stove.
Step 2
Meanwhile, in a large sauté pan or pot, add the oil and place over medium heat. Add the sliced onion to the pan with a pinch of kosher salt and sauté over medium heat until translucent or lightly brown, about 5 minutes. Add half the can of chipotles in adobo or about 1/4 cup including two or three of the chilies. (If you are really sensitive to heat, add just a tablespoon or two of the sauce. You can always add more.) Stir for a minute until the onions are nicely coated in the sauce, then add the tomatoes and chicken stock. Season with a pinch of salt.
Step 3
Let the sauce simmer over low heat while you pull the chicken meat from the skin and bones. Shred the meat and add to the sauce. (Discard the skin; place bones in the reserved cooking liquid and let simmer for a couple of hours. Strain, and transfer the stock to storage containers. Refrigerate overnight. The following day, scrape off the fat and discard. Freeze stock.)
Step 4
Bring the pan with the chicken to a simmer and let cook for 15 minutes over low heat. Coarsely chop the cilantro, add to the pot and stir to incorporate. Taste mixture, add more salt if necessary. You can pull out any chipotles that are still intact or you can just avoid pulling them from the mixture when you are serving.
Step 5
Serve with heated tortillas, grated cheese, lime wedges, chopped onion and sour cream on the side.