Chipotle Salsa Baked Chicken


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

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Showing 4 of 72 Comments

  • 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!

  • Lisa

    Hi Elise! I have been enjoying your website and recipes for a couple of years now. I love the fact that you include beautiful photos with every recipe, and you have set up a very concise way to look up recipes by category, etc. I have you bookmarked!

    Anyway, I saw this recipe a few weeks ago and wanted to give it a try. It is absolutely delicious! The flavors of this dish are so deep and smoky. I decided to add just a little more garlic, and at your suggestion to “add more of the Chipotle to taste”, so I added 1 more Chipotle pepper and used 1 tablespoon of the adobo sauce instead of the 1 teaspoon since I love that flavor. I also added a bit more of the lime juice because of the addition of the extra Chipotles. The combination of all of the flavors of the sauce is phenomenal. I think next time though I will drain the tomatoes since the excess sauce in the bottom of the baking dish was a little thinner than I expected, although the sauce on top of the chicken itself was perfect. I think the liquid from can of tomatoes must have settled in the bottom of the dish. Also, I will probably sauté the chicken with some canola or olive oil, just to get a nice sear on the outside before placing the pieces in the baking dish since my chicken thighs took a little longer that 30 minutes to cook. I served the chicken with some of your suggestions; sour cream (a must in my opinion to accompany the smoky flavor of the sauce), diced avocado and cilantro. I also served grilled flour tortillas and black beans on the side. We ate half of our plated chicken in the tortillas with the garnishes, and the other half without the tortillas. Both ways were equally as good. Thank you for such a flavorful recipe and one that is so quick to put together on a weeknight! I will be making this dish again and again. Please keep the great recipes coming!

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