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Bring a large Dutch oven up to heat over medium. Add in the oil followed by the onions and sauté until golden brown, about 5 minutes. Next add in the garlic and cook for 1-2 minutes.
Add in the chicken thighs and season liberally with salt and pepper. Next add in the canned tomatoes, stock, chipotles, and chipotle sauce.
Stir to combine, cover, reduce to a low simmer and cook for 2 ½ to 3 hours, stirring occasionally.
Remove the lid during the last hour of cooking so the liquid reduces into a thick sauce. Break up the larger pieces of chicken with the back of a wooden spoon or with 2 forks. Taste and season with salt and pepper then squeeze in the lime juice.
Serve inside warm tortillas with cheese, lettuce, avocado and sour cream.
Recipe Adapted from Food & Wine.