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Mexican Stuffed Peppers - Three Ways {Vegan, Vegetarian, and Omnivore}

These Mexican Stuffed Peppers are easy to customize for vegan, vegetarian, and omnivore eaters. A simple base of black beans, rice, and tomatoes is combined with either vegan chipotle cheese sauce or a dairy version (see Recipe Notes). Optionally, for the meat eaters, add in some spicy chorizo. Uses the Mother Mix.
Prep Time15 mins
Cook Time40 mins
Total Time55 mins
Course: Main Course
Cuisine: American, Mexican, Spanish
Keyword: best stuffed peppers, chipotle cheese recipe, chipotle cheese stuffed peppers vegan, chipotle cheese stuffed peppers vegetarian, chipotle cheese stuffed peppers with meat, chipotle cheese stuffed peppers with rice, easy stuffed peppers, chipotle cheese sauce, vegan chipotle cheese sauce, easy weeknight dinner, stuffed chili pepper, stuffed peppers plant-based, stuffed peppers vegan, stuffed peppers vegetarian, stuffed peppers with chorizo, stuffed peppers with meat, stuffed peppers with rice, the mother mix, vegan stuffed peppers, vegetarian stuffed pepper
Servings: 12 1/2 peppers
Calories: 134kcal
Author: sylvia


  • 6 peppers {See Recipe Notes}
  • 1 cup cooked rice
  • 2 cups cooked black beans
  • 2 cups diced tomatoes {Fresh or canned. If using canned, drain them first.}
  • 1 tsp garlic powder
  • 1-2 tablespoons chipotles in adobe sauce
  • 1 1/3 cups Mother Mix + 2 cups water {See Recipe Notes for link}

Optionally, if you do not have Mother Mix

  • 1 cup almond flour {also known as super-fine almond meal, or ground blanched skinless almonds}
  • 2 cups water
  • 4 tablespoons tapioca starch
  • 2 tablespoons, plus 2 teaspoons nutritional yeast nutritional yeast
  • 1 teaspoon salt

Optionally, if you want to make with dairy-based chipotle cheese sauce, see Recipe Notes (it's easy!)

    If making omnivore version

    • 1/3 cup chorizo sausage meat, per carnivore

    For topping

    • 2 tablespoons cheese/cheeze of choice, per each pepper
    • sour cream
    • cilantro


    • Preheat the oven to 350F.
    • Slice the peppers in half from stem to bottom. Remove the seeds and lay the peppers cut side up on a baking sheet or pan. 
    • Make the base mixture by combining the rice, black beans, tomatoes, and garlic powder in a large bowl.
    • See the Recipe notes if you want to make this using my dairy-based cheese sauce.
      Otherwise, make the chipotle cheese sauce, by combining either the Mother Mix plus water and chipotles OR the individual cheese sauce ingredients plus chipotles in the blender.
      Blend on high for one minute.
      Transfer to a medium saucepan and cook and stir over medium heat until cheese sauce is thick and stretchy, 6-7 minutes. 
    • Stir the chipotle cheese sauce into the base mixture. 

    If making the omnivore version:

    • Pan fry the sausage meat, breaking up any large chunks. Drain off the excess oil. 
    • If you want all of the peppers to have meat, then just add the meat to the cheese/bean/tomato mixture and then stuff the peppers. 
    • If you want to make some stuffed peppers omni-friendly and some not, then separate out about about 1/2 cup of base mixture per 1/3rd cup meat. 

    For all versions:

    • Spoon the mixture into the peppers so it's level with the edge of the pepper. 
      Green, red, and yellow peppers, cut from stem to tip, and stuffed with rice, beans, tomatoes, and chipotle cheese sauce mix.
    • Cook at 350F for 30-40 minutes, until the pepper is starting to get soft. 
      Remove from oven and top each pepper with about 2 tablespoons of cheese. 
      Return to oven until cheese is melted, 5-10 minutes. 
    • Serve with a big dollop of {vegan} sour cream, and garnish with cilantro if desired. 


    Pepper Quantity 
    Obviously, peppers are not all uniform in size. For this recipe, I am allowing about 1/2 cup of filling per 1/2 pepper. Your mileage may vary. If you end up having filling left over, you can freeze it until you have more peppers. 
    Choosing Peppers
    Typically, I just use bell peppers for this recipe, but if you like Poblano peppers this make another good option. Poblano peppers, also known as Ancho peppers, have a little bit of heat to them, so keep that in mind if you are choosing to add more spices to the stuffing mix. 
    Tip for Feeding Mixed Groups
    I usually buy 3 different coloured peppers. I use the green peppers for the vegan version, orange or yellow for vegetarian, and red for the version with meat in it. 
    Option to Use Dairy-Based Chipotle Cheese Sauce 
    If you are vegetarian or omnivore, you can swap out the Mother Mix cheese sauce with dairy-based cheese sauce. Follow the Simple Cheese Sauce recipe, but before you add the milk to the pot, first blend the milk with the chipotle peppers, and then stir it into the flour/butter mixture. 
    Storage, Reheating, and Freezing 
    You can make these a couple of hours ahead of time, either up to the point of baking them, or up to the point where you are about to add the final cheese/cheeze topping. Refrigerate them until you are ready to do the final cooking. 
    These are really good reheated. I actually like them better the next day as the pepper gets really nice and soft.
    You can freeze the cooked versions. Ideally freeze them without the final cheese topping, defrost them, heat them in a 250F oven for about 20 minutes until hot, and then add the final cheese topping. 

    About the Mother Mix

    The Mother Mix is a simple DIY dry mix that gives you a jumpstart on a number of recipes on this site. It’s vegan and gluten-free and made from all-natural ingredients. You can find the recipe for this awesome pantry staple here. 
    Amp it Up a Notch
    I purposely made this recipe super simple so that it would be fairly fast to make if you are making all three variations. If you aren't in a hurry, you could use fresh garlic instead of dried, fry up some onions to go into the mix, and/or add in other vegetables like corn or roasted red peppers. If you are vegan/vegetarian but want it be more meaty, you could add in some veggie ground round, mock sausage, or TVP (aka soy mince.) 
    Nutritional Information
    Nutrition information is an estimate based on the vegan version of the recipe, without cheese topping or garnishes. 


    Calories: 134kcal | Carbohydrates: 17g | Protein: 6g | Fat: 4g | Sodium: 221mg | Potassium: 233mg | Fiber: 4g | Sugar: 1g | Vitamin A: 95IU | Vitamin C: 3.9mg | Calcium: 42mg | Iron: 1.6mg