A colourful array of stuffed peppers, green, yellow, and red, topped with cheese, sour cream, and cilantro. From the recipe: Stuffed Pepper Three Ways - Vegan, Vegetarian, Omnivore

Chipotle Cheese Stuffed Peppers – Three Ways {Vegan, Vegetarian, Omnivore}

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4 minute cheeze, carnivore, cheeze, dinner, egg free, get your vegetables in!, plant-based, reducetarian, three ways, vegan, vegetarian

This oooey-gooey, make’em anyway you want’em Chipotle Cheese Stuffed Peppers recipe, featuring a super simple mix of rice, black beans, and tomatoes all tied together with a mildly spicy chipotle cheese sauce, and then topped with your choice of cheese/cheeze. This recipe is my most flexible entree to date — you can make these Chipotle Cheese Stuffed Peppers 100% plant-based, 100% vegetarian, or 100% omni-friendly, or of course you can make all three versions, and the recipe is simple enough that it’s very little extra work to do so.

Beyond being super flexible in terms of diet types, these stuffed peppers are easy to make ahead, taste even better reheated, and yes you can freeze them!

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Chipotle cheese stuffed red peppers, with rice, beans, chorizo, and chipotle cheese sauce, topped with cheese and sour cream. All on a white plate.

Chipotle Cheese Stuffed Peppers – Omnivore Version


Three chipotle cheese stuffed green peppers, with rice, beans, and chipotle cheese sauce, topped with cheese and sour cream, and cilantro. All on a light blue plate, sitting on the countertop.

Chipotle Cheese Stuffed Peppers – Vegan Version

Eating Together Made Easy

If you don’t know it yet, you soon will, here at not not nutritious I am fixated on making it easier to cook for diverse groups of eaters, from plant-based peeps/vegans to vegetarians, and omnivores.

The common ground for this recipe are the peppers themselves, along with a trio of rice, black beans, and tomatoes. Tying it all together is the chipotle cheese sauce. I’ve got a vegan version that’s a variation of my 4 minute cheeze sauce and a vegetarian version that’s an easy add-in to my simple cheese sauce.

If you’re vegetarian or omnivore and you’re feeling adventurous, go “not not” style — that is, make the vegan version and then add a final topping of dairy-based cheese. That’s what we do at my house and besides being fast and delicious, it’s a great way to reduce your dairy consumption. And yes, in case you’re wondering, cheeze and cheese work together very nicely.

TIP: If you’re making multiple versions, use different coloured peppers to help keep track of which version is which. I typically use green peppers for the vegan version, yellow or orange peppers for the vegetarian, and red ones for the meat-eaters version.

Exhibit A: The green ones are actually Poblano peppers, but any green pepper would do.

A colourful array of chipotle cheese stuffed peppers, green, yellow, and red, topped with cheese, sour cream, and cilantro. From the recipe: Stuffed Pepper Three Ways - Vegan, Vegetarian, Omnivore

Chipotle Cheese Stuffed Peppers

Etiquette Note

I wanted to display all of the variations of the stuffed peppers in a single photo, so I’ve put all the peppers on a single plate. Consider your crew’s preferences; some people might prefer to have separate cooking and serving dishes for different versions.

Here we go! Chipotle Cheese Stuffed Peppers for the People!

Chipotle Cheese Stuffed Peppers - Three Ways {Vegan, Vegetarian, and Omnivore}
Prep Time
15 mins
Cook Time
40 mins
Total Time
55 mins

These Chipotle Cheese 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. 

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, vegan stuffed peppers, vegetarian stuffed pepper
Diet: omnivore, reducetarian, vegan, vegetarian
Servings: 12 1/2 peppers
Calories: 134 kcal
Author: Sylvia E
  • 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 4 minute cheeze sauce mix + 2 cups water {See Recipe Notes for link}
Optionally, if you do not have 4 minute cheeze sauce mix
  • 1 cup almond flour {also known as almond meal, or ground blanched 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
  1. Preheat the oven to 350F.

  2. 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. 

  3. Make the base mixture by combining the rice, black beans, tomatoes, and garlic powder in a large bowl.

  4. 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 4 minute cheeze sauce 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. 

  5. Stir the chipotle cheese sauce into the base mixture. 

If making the omnivore version:
  1. Pan fry the sausage meat, breaking up any large chunks. Drain off the excess oil. 

  2. 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. 

  3. 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:
  1. 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.
  2. 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. 

  3. Serve with a big dollop of {vegan} sour cream, and garnish with cilantro if desired. 

Recipe Notes
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 cheeze 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. 

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. 

Nutrition Facts
Chipotle Cheese Stuffed Peppers - Three Ways {Vegan, Vegetarian, and Omnivore}
Amount Per Serving
Calories 134 Calories from Fat 36
% Daily Value*
Total Fat 4g 6%
Sodium 221mg 9%
Potassium 233mg 7%
Total Carbohydrates 17g 6%
Dietary Fiber 4g 16%
Sugars 1g
Protein 6g 12%
Vitamin A 1.9%
Vitamin C 4.7%
Calcium 4.2%
Iron 8.7%
* Percent Daily Values are based on a 2000 calorie diet.

PIN: Chipotle Cheese Stuffed Peppers – Three Ways

A colourful array of chipotle cheese stuffed peppers, green, yellow, and red, topped with cheese, sour cream, and cilantro. From the recipe: Stuffed Pepper Three Ways - Vegan, Vegetarian, Omnivore

Chipotle Cheese Stuffed Peppers – Three Ways

Other Two and Three Ways

Looking for some other mains to feed mixed eaters? How about:

Behind the Scenes: Taking Pics of Chipotle Cheese Stuffed Peppers

Here’s a snap that Mikael took of me taking pictures for this post. I took SO many photos of these stuffed peppers! I actually started this recipe 6 months ago, took pics, and was not happy with them at all. So, I tried again a few days later. Still not happy. Then life ensued, and finally I got back to this post and once again, took a whole slew of photos. I’m still not very happy but at some point you have to just let things go. Cheese is hard, people! And vegan cheeze, yeah, no, it really does not look that pretty.

not not nutritious site owner, Sylvia Eastman taking photos of stuffed peppers

Behind the Scenes


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