Chipotle Salsa Baked Chicken

Chicken breasts or thighs, smothered in chipotle salsa, topped with Monterey jack cheese, and baked.

Chipotle Salsa Baked Chicken
Elise Bauer

Dear restaurant chain by the same name, thank you for making chipotle a household word!

(And for helping to teach people how to say it correctly—"chee POAT leh".)

I love cooking with chipotles—smoked, dried, red jalapeños—especially those packed in adobo sauce.

In this recipe we are making a simple salsa with fire roasted tomatoes, onions, lime juice, and chipotles packed in adobo, coating chicken breasts with the sauce, topping them with melty jack cheese, and baking them in the oven in a casserole dish.

So easy! And so versatile.

Chipotle Salsa Baked Chicken
Elise Bauer

First, chiles in adobo last a long time in the fridge, many months once you've opened the can, so you don't have to stress about using them up right away. Second, this dish has lots of sauce, which tastes great with rice, pasta, tortillas, even chips. Third, it makes great leftovers.

This chicken bake is very similar to my salsa verde baked chicken, but with a smokey chipotle salsa instead. It's a little on the acidic side with the lime juice and adobo, and tastes great with avocados to cut the acid and the heat.

While I usually serve it with rice, it's also surprisingly good with penne pasta. In fact I could see making this again as a pasta casserole, just chop up the chicken to bite sized pieces, toss with cooked pasta and the salsa, sprinkle with cheese and bake until the chicken is cooked through.

Chipotle Salsa Baked Chicken
Elise Bauer

A big shout out and thank you to my friend Gaby Dalkin, from whose chipotle salsa recipe I (barely) adapted this one.

Chipotle Salsa Baked Chicken

Prep Time 10 mins
Cook Time 35 mins
Total Time 45 mins
Servings 6 servings

This casserole produces a lot of sauce! Use it to spoon over rice or pasta, or for dipping tortilla chips.


  • 1 (15-ounce) can fire roasted tomatoes (or canned whole or crushed tomatoes if fire roasted are not available)

  • 1/4 cup red onion, chopped

  • 1 clove garlic, chopped

  • 1/2 cup packed fresh cilantro, chopped

  • 2 chipotle chili peppers in adobo, plus 1 teaspoon adobo sauce (less or more to taste)

  • 1 teaspoon lime juice

  • 1 teaspoon kosher salt

  • 1 1/2 pounds boneless, skinless chicken breasts (or thighs), trimmed of excess fat, cut into 3-inch-wide pieces

  • 4 ounces Monterey Jack cheese, grated or sliced

Serve with or over:

  • Avocados

  • Chopped cilantro

  • Sour cream

  • Corn or flour tortillas

  • Rice

  • Pasta


  1. Make the salsa:

    Place tomatoes, onion, garlic, cilantro, chipotle peppers and adobo, lime juice and salt in a blender or food processor. Pulse a few times so there are no more large chunks of anything, but not so much so that the salsa is completely smooth.

  2. Spread salsa over chicken:

    Preheat the oven to 350°F. Place the chicken pieces in a casserole dish, just large enough to fit them all in a single layer (about 8x10-inches). Spread the chipotle salsa over the chicken pieces, turning the chicken pieces to coat them all over with the salsa.

    Elise Bauer
    Elise Bauer
  3. Bake, layer with cheese, bake again:

    Cover with aluminum foil and bake for 25 minutes (30 minutes for thighs). Remove the foil, and sprinkle or layer the cheese over the chicken. Bake uncovered for 10 minutes more.

    Serve over rice, pasta, or with tortillas on the side, along with chopped avocado, more cilantro, crema fresca or sour cream.

    Variation: This is a bake-in-the-oven recipe. You could easily adapt the recipe to the stovetop this way: sear the chicken pieces first in a little olive oil, remove the chicken, add the onions to the pan, cook them till soft, add the garlic and chiles, cook a little longer, add the tomatoes, lime juice, cilantro, and salt, then add the chicken, coat the chicken with the sauce, bring to a low simmer, cover, cook for 25 minutes, sprinkle with cheese, cover and cook for a few more minutes until the cheese is melted.


Homemade salsa with tomatoes and chipotle from What's Gaby Cooking

Chipotle chicken tacos from Lisa Fain, the Homesick Texan

Chipotle chicken and corn chowder from Brown Eyed Baker

Chipotle Salsa Baked Chicken
Elise Bauer
Nutrition Facts (per serving)
289 Calories
10g Fat
7g Carbs
41g Protein
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Nutrition Facts
Servings: 6
Amount per serving
Calories 289
% Daily Value*
Total Fat 10g 13%
Saturated Fat 5g 24%
Cholesterol 113mg 38%
Sodium 545mg 24%
Total Carbohydrate 7g 3%
Dietary Fiber 2g 6%
Total Sugars 4g
Protein 41g
Vitamin C 9mg 45%
Calcium 190mg 15%
Iron 2mg 13%
Potassium 556mg 12%
*The % Daily Value (DV) tells you how much a nutrient in a food serving contributes to a daily diet. 2,000 calories a day is used for general nutrition advice.
Nutrition information is calculated using an ingredient database and should be considered an estimate. In cases where multiple ingredient alternatives are given, the first listed is calculated for nutrition. Garnishes and optional ingredients are not included.