Chipotle Chicken

Zest up your baked or grilled chicken with this easy chipotle marinade. This bright blend of smoky flavors and fresh citrus is a real winner. The chipotle chicken is very tender and flavorful and the crispy skin is irresistible. I’ve given instructions for baking, grilling and air-frying the chicken thighs so they’ll come out perfect every time.

ingredients for the chipotle marinade.

A chipotle marinade for juicy, flavorful chicken

My husband loves Mexican food, so I always want to jazz-up our weeknight chicken with Mexican, Southwestern or Tex-Mex flavors. This easy Mexican-inspired chicken marinade has become one of my go-to’s because I can make it the night before (or even in the morning, before work). The chicken hangs out in the chipotle marinade all day to soak up the goodness before popping it into the oven or tossing it onto a hot grill.

Steve Raichlen is one of my husband’s grilling and barbecue idols. (Mine too). With countless cookbooks and even a Barbecue University (how cool is that?)– his easy, do-able recipes and techniques always deliver big flavors and acclaim from our diners.

This chipotle chicken is based on one of his amazing recipes and all of the ingredients are probably in your pantry already.

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Ingredients for chipotle chicken marinade

  • Canola Oil
  • Plum Tomatoes
  • Onion
  • Garlic
  • Ground Cumin
  • Black Pepper
  • Dried Oregano
  • Kosher Salt
  • Fresh Lime Juice
  • Fresh Orange Juice
  • Canned Chipotle Peppers
  • Adobo Sauce from the can
  • Red Wine Vinegar
  • Honey

What are chipotle peppers?

Chipotle peppers are jalapeños that have been left on the vine to fully ripen (they go from green to red as the mature). The jalapeños are smoked, then dried. Chipotle peppers are used primarily in Mexican and Southwestern or Tex Mex cooking.

What is chipotle in adobo?

Chipotles in adobo are rehydrated chipotle peppers packed in a tangy puree of tomato, garlic, onion and spices. The adobo itself is very spicy but balanced. Chipotle peppers stay tender and moist in the adobo, so they’re ready to use straight from the can and give the Mexican chicken marinade a deep, rich balanced flavor.


Be careful when handling the chipotle peppers and adobo. The oils from the pepper and sauce can stick to your hands (even after you’ve washed them) so take care not to touch them directly and if you do, keep your hands out of your eyes and away from babies or pets. The burn is real.

fresh squeezed orange and lime juice and spices for the chicken thigh marinade.

This marinade comes together in about 30 seconds once the ingredients have been prepped — and the prep is pretty simple.

Prepping ingredients for the Mexican chipotle marinade:

  1. First, juice one or two fresh limes and about half of one orange. Measure the juices and set aside.
  2. Char the vegetables in a heavy skillet or cast iron pan. I have a small cast iron pan that works well for this.
  3. Add a touch of Canola oil to the hot skillet and add the whole cloves of garlic with the peels still on, the wedge of onion and the plum tomatoes. Cook until the the outside of the veg is charred and the vegetables have softened. (The garlic takes about 4-5 minutes, and the veg will take 10-12).
  4. Flip the vegetables with a pair of tongs to ensure that all sides get some color and char.
  5. Peel the charred garlic cloves and add to a mini food processor.
  6. Transfer the cooked veg to the food processor and add the citrus juices, spices, chipotle peppers and other ingredients and pulse several times until smooth.
charring the vegetables and processing the chipotle marinade in a mini food processor.

Marinating the chicken

Now that the marinade is done, it’s time to give the chicken a good, long soak.

I recommend at least 8 hours or overnight. I’ll be honest, I’ve let my chicken thighs soak for up to two days and they just get better and better in this chipotle marinade, so don’t skimp on the immersion time.

The smoky chipotles really permeate the chicken and flavor the meat and skin while the acid from the fresh citrus help to tenderize and give a tanginess to the meat.

Trim the chicken, place in a Zip Top bag and pour the marinade over.

Trim the excess fat and skin from the chicken

We all like crispy skin on our grilled or baked chicken, but sometimes it’s too much.

You want a layer of skin to cover the meat and keep it moist as it cooks, but it shouldn’t be hanging off of the chicken.

Before adding the thighs to the chipotle marinade, evaluate how much extra skin and fat there is. (Based on my supermarket’s affinity for charging extra for what I don’t need, I’m betting you’ll have a fair amount too).

If your chicken thighs come with a large, excess flap of skin, trim it off.

Seal the chicken thighs and chipotle marinade in a Zip Top bag to rest overnight.

You can marinate the chipotle chicken in a large bowl, a resealable plastic bag or one of these reusable Zip-Top containers. The 32-ounce size (pictured above) held the chicken and the chipotle marinade for this recipe and wholly submerged the protein. Perfect.

If you haven’t gotten a set of these yet, what are you waiting for? Here’s my affiliate link and you can also enter below for a chance to win a complete set of Zip Top containers in your choice of colors.

Dry the chicken thighs thoroughly and bake them on a rack in a hot oven to get the skin crispy. Before and after photos.

Ways to cook the chicken

You can bake, grill or even air fry chipotle marinated chicken. Whatever is more convenient for you.

For this batch I actually baked two of the marinated chicken thighs in the oven and grilled the other two. Both methods were simple to do and gave excellent results. It will work equally well in the air fryer. (Instructions for all three methods given in the recipe card).

Pro-Tips for cooking the chicken thighs

  • Remove the marinating chicken about half an hour before cooking to take the chill off the chicken.
  • Use paper towels to dry the chicken completely before cooking. If the chicken skin is wet, it will steam instead of crisp.
  • Preheat your oven or grill before cooking the chipotle marinated chicken thighs.
  • For the oven: line a rimmed baking sheet with foil to catch drips and place the chicken thighs on a rack over the baking sheet. This will allow the hot air to surround the chicken when cooking.
  • If you’re using the grill or air fryer, use tongs to turn the chicken, not a fork. The fork will pierce the skin and juices will escape.

Grilling the chipotle adobo chicken also allowed the poultry to take on some of the charred grill marks (flavor), which gets extra credit, but overall, both cooking methods yielded similar results.

grilling the chicken on the weber gas grill.

The taste test

A side-by-side taste comparison between the baked and grilled chipotle chicken gave equally high marks for extra crispy skin and tender, juicy chicken.

Flavor-wise, the Mexican chipotle chicken marinade stands out. The smoky peppers aren’t overly spicy. Fresh lime, orange juice, and red wine vinegar add a tangy bite to the chicken, and the dried spices amplify the smoky, lively flavors.

When eating chicken thighs, I usually start with a knife and fork, but I invariably pick up the chicken and nibble the meat right from the bone. With this lip-smacking marinade, my husband and I were also licking our fingers to get every morsel of the smoky pepper marinade from the bones.

Chipotle marinated chicken FAQ’s

Can I make the Mexican chipotle marinade in advance?

Yes! You can make this marinade up to 3 days in advance. Store in the refrigerator in a glass container with a tight fitting lid.

Can I freeze the chipotle chicken marinade?

Yes. It should keep for up to 2 to 3 months in the freezer. Defrost before marinating the chicken.

Can I use Mexican chipotle marinade for other meats?

Absolutely! This is very good on pork and beef, but try it on other meats or even tofu for a change of pace.

How long will leftover marinated chicken last in the fridge?

The chicken should be good for 5 days if it’s well-wrapped and chilled.

How do I reheat the chipotle chicken?

Preheat the oven to 300°. Place the chicken on a baking tray coated with vegetable spray and heat for 10-15 minutes or until warmed through.

Cutting into juicy baked chicken thighs with chipotle marinade.

What to serve with:

What can I do with leftovers?

  • Make a chipotle chicken bowl with cooked rice, tomatoes, red onion, avocado and black beans.
  • Grill a chipotle chicken avocado melt by chopping leftover meat and piling it on sourdough bread with cheddar and monterey jack cheese, slices of avocado and a spoonful of red pepper aioli.
  • Make a chipotle chicken quesadilla by layering chopped leftover meat with grated monterey jack cheese and a spread of refried beans. Serve it with pico de gallo.
  • Make a spicy chicken chipotle pasta with cooked farfalle, queso fresco, chopped bell pepper and 2 cups of creamy bechamel sauce spiked with ? cup of the chipotle marinade. (Reserve the marinade before adding it to the chicken).
grilled chipotle chicken thighs on a plate.

More easy chicken recipes you might like:

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chipotle marinated chicken thighs served with broccoli and heirloom tomatoes.
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5 from 3 votes

Chipotle Chicken

This spicy, smoky, citrusy chipotle marinade gives chicken a juicy, flavorful bite. Cook the chipotle chicken in the oven, on the grill or in an air-fryer. This marinade is also good for pork and beef.
Author: Lisa Lotts
Course Main Course
Cuisine Mexican
Keyword chicken thighs, chipotle
Dietary Restrictions Dairy-Free, Egg Free, Gluten-Free
Prep Time 20 minutes
Cook Time 20 minutes
Total Time 8 hours 40 minutes
Servings 4


  • Mini Food Processor or Blender



  • 1 teaspoon canola oil
  • 2 plum tomatoes
  • ¼ medium onion
  • 2 cloves garlic
  • ½ teaspoon ground cumin
  • ½ teaspoon ground pepper
  • ½ teaspoon dried oregano
  • ½ teaspoon Kosher salt
  • ¼ cup fresh lime juice
  • 2 tablespoons fresh orange juice
  • 1 tablespoon red wine vinegar
  • 2 canned chipotle peppers + 1 teaspoon adobo from the can
  • 1 tablespoon honey


  • 1 ½ pounds chicken thighs or other cuts of poultry.
  • chipotle citrus marinade


  • fresh cilantro leaves
  • lime wedges


  • Heat the canola oil in a small heavy pan or cast iron skillet over medium high heat. When the pan is hot, add the unpeeled cloves of garlic, whole plum tomatoes and the onion. Cook, turning occasionally until there’s a warm char on the vegetables. Note: the garlic should be ready in about 4-5 minutes, while the tomatoes and onions will take 9-10. Set aside.
  • Peel the skins from the garlic and add them to the food processor or blender. Add the charred vegetables, cumin, pepper, dried oregano and kosher salt.
  • Squeeze the juice from the limes and orange (you may need 1 ½ to 2 limes depending on how juicy they are. Add the lime and orange juice to the vegetable mixture followed by the vinegar, chipotle peppers, adobo and honey.
  • Blend until smooth. Chipotle marinade can be made ahead of time. Keep it refrigerated for up to 10 days in a sealed glass jar.


  • Trim any excess skin from the chicken and transfer it to a large container to marinate.
  • Refrigerate for at least 8 hours.


  • About ½ an hour before baking, remove the chicken from the marinade and pat dry with paper towels.
  • Preheat the oven to 400° F. Line a baking sheet with foil (to cut down on the mess). Place a wire rack over the foil and lightly spray with vegetable spray.
  • Transfer the thighs to the wire rack and bake for 30-35 minutes or until the skins are crispy and the meat is cooked through and internal temperature is 165° F.


  • Preheat the grill to a medium high temperature (about 400°). Place the chicken skin side down on the grill and cook for 10-12 minutes with the lid on the grill. Watch for flare-ups and be ready with a squirt water bottle in case.
  • Use grilling tongs to flip the chicken and cook for an additional 10-12 minutes. Flip the chicken one additional time and finish cooking for 3-5 or until the internal temperature reaches 165°F. Use a digital thermometer to be sure.


  • Heat the air fryer to 380° F. Pat the chicken dry and add to the basket skin side down. Cook for 10 minutes, then flip and continue cooking for another 10 minutes. Turn the chicken thighs one final time and cook for an additional 5-7 minutes or until the internal temperature registers 165° F on a digital thermometer.


  • Transfer the chicken to a serving platter and let rest for 5 minutes to allow the juices to redistribute throughout the meat.


You can double the recipe and use whatever chicken pieces you like. Cooking times will vary depending on how large chicken pieces are and whether they are bone-in, skin-on or boneless.


Calories: 1694kcal | Carbohydrates: 44g | Protein: 113g | Fat: 118g | Saturated Fat: 31g | Polyunsaturated Fat: 25g | Monounsaturated Fat: 50g | Trans Fat: 1g | Cholesterol: 667mg | Sodium: 2081mg | Potassium: 1952mg | Fiber: 6g | Sugar: 28g | Vitamin A: 3198IU | Vitamin C: 56mg | Calcium: 129mg | Iron: 7mg

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  1. 5 stars
    Looks like this is going to hit my table this week!!

  2. 5 stars
    These containers are very unique. The most useful way I can see for these is pouring from the container, which you mention with the marinade.

  3. Paula Rothman says:

    5 stars
    Want to try this with some chick’n meat substitute.