Chipotle Salsa Baked Chicken

Photography Credit: 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

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

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 Recipe

  • Prep time: 10 minutes
  • Cook time: 35 minutes
  • Yield: Serves 6

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 chopped red onion
  • 1 clove garlic, chopped
  • 1/2 cup, packed, chopped fresh cilantro
  • 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 pound boneless, skinless chicken breasts (or thighs), trimmed of excess fat, cut into 3-inch wide pieces
  • 4 ounces grated or sliced Monterey jack cheese

Serve with or over

  • Avocados
  • More chopped cilantro
  • Sour cream
  • Corn or flour tortillas
  • Rice
  • Pasta


1 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 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.

chipotle-salsa-baked-chicken-method-1 chipotle-salsa-baked-chicken-method-2

3 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.

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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

Showing 4 of 68 Comments

  • Tina

    Be sure to cut them down to size because, after 25 minutes, mine was still raw. I cut them the right size width-wise but my chicken must have been substantially thicker. It turned into a marathon of waiting to eat until way too late in the evening. I ended up eating something else for dinner that night.

  • Paula

    Just made this tonight as written. Very good recipe. Taste like it was from a Mexican restaurant. I like spicy and will say 2 of the chilies in adobe sauce was the right amount. It was spicy but not over the top!

  • Sandy

    Fabulous! I made this tonight and my husband can’t stop raving about it. I shredded the leftovers before putting them away and now we’re looking forward to some amazing nachos tomorrow night.

    Next time I might make the salsa the night before to make it even quicker. Can I assemble the chicken through the cover-with-foil step? Or is that a no-no with raw chicken?

    Thanks, Elise, for this wonderful recipe. So often I feel like weeknight cooking is a choice between easy and flavor, but this is full-flavored AND incredibly easy. Now I can’t wait to try the salsa verde chicken bake.

  • Amy

    This was amazing!! The salsa is wonderful by itself and the chicken was really flavorful. I used crushed fire roasted tomatoes and I broiled it without the foil for no real reason other than the fact that I make a similar Italian cheesy baked chicken dish that is broiled and I just like the way the chicken comes out cooked that way. I did not find the salsa to be watery cooking in this manner. Thanks Elise for another great recipe. I have been a fan of your site since I found your instructions for how to make hard boiled eggs 5 years ago :) You have saved the day many times over the years with your recipes!

  • Amber

    Elise – Making this tomorrow and wondering if you’ve ever added Yukon Gold potatoes? I thought they’d be a great addition, and would soak up some of that yummy chipotle salsa!

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