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Pat the chicken dry. Sprinkle both sides of the chicken with salt and pepper. Heat a large skillet over medium high heat and add the olive oil. When the oil is hot add the chicken. Cook for about 4 minutes, then flip. Cook for another 3-5 minutes until no longer pink in the middle, or until a thermometer reads 165 degrees. Remove, let cool, and shred with 2 forks. Set aside.
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In the same skillet that you cooked the chicken in, add 1 tablespoon olive oil and set over medium heat. Add the chopped onions and chipotle. Cook until onions are mostly translucent, about 3-4 minutes.
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Add the garlic, cumin, cinnamon, cloves, and coriander. Cook for another 3 minutes or so.
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Add the pinto beans and whole tomatillos. Cook for about 5 minutes, breaking up the tomatillos and some of the beans with a wooden spoon.
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Add the cooked chicken and cook for another couple minutes. Turn off the burner and remove from heat.
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In a hide-sided skillet, add about a 1/2 inch of oil. Set over medium heat. After about 5 minutes, test it by tossing in a little piece of tortilla. If the tortilla bubbles immediately, then the oil is hot enough. If not, wait longer.
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Cover the tortillas and heat them in the microwave for 30 seconds to 1 minute. You just want to get them pliable enough to be able to fold them.
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Add a large spoonful of the filling into the center of a tortilla. Fold it up (see photos) and secure with a toothpick.
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Fry the chimichangas 2 at a time. Cook for 2-3 minutes on the first side, then flip and do another 2-3 minutes on the other side. It is done when the tortilla is a light golden brown. Remove to a paper-towel-lined plate.
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Serve hot with pico de gallo, guacamole, sour cream, queso fresco, cilantro, and fresh limes.