Add the ingredients for the marinade to a small food processor, food chopper, or small blender. Blend until a thick paste forms. If you don’t have a small apparatus for blending food, you can finely chop everything with a sharp knife and mix the marinade ingredients together in a small bowl.
Transfer the raw chicken thighs and the chipotle chicken marinade to a large zip lock bag or a large bowl. Seal the bag (or cover the bowl with plastic wrap) and swish everything around until the chicken pieces are well-coated in marinade. Marinate the chicken in the refrigerator for at least 20 minutes, ideally overnight.
Bring the marinated chicken out of the refrigerator and place it on the counter to allow it to come to room temperature about 15 to 20 minutes prior to cooking. This ensures the chicken cooks evenly so that it gets a nice sear on the outside while cooking the inside.
Heat a large skillet (both a cast iron skillet or a large nonstick skillet work) over medium-high heat with 1 to 2 tablespoons of avocado oil (or cooking oil of choice), or enough oil to coat the surface of the skillet. Note: a grill pan, an outdoor grill, or air fryer work too.
Allow the skillet to heat up for a few minutes until it becomes sizzling hot.
Carefully transfer the marinated chicken thighs to the hot skillet and cook for 6 to 8 minutes, or until a golden-brown crust forms. Flip and cook for another 6 to 8 minutes, or until the chicken is cooked through.
Insert a meat thermometer into the thickest part of each chicken thigh to verify the internal temperature. Chicken is safe to eat once it has reached an internal temperature of 165 degrees F or higher. Chicken thighs generally taste best with the best texture after reaching 185 degrees Fahrenheit. Place chicken on a large cutting board and let the chicken rest for 10 minutes.
Use a sharp knife to cut the chicken into slices, or chop it into small pieces.
Serve chipotle chicken with your choice of side dishes or use it in burrito bowls, burritos, or salads. I love making chicken burrito bowls with cilantro lime rice, corn salsa, guacamole, homemade salsa, black beans, fajita veggies (sauteed onions and bell peppers) and grated cheese. I find these toppings closely mimic what you get at the Chipotle restaurant.