stuffed peppers with butternut squash and quinoa in a white baking dish topped with chopped parsley and basil leaves

Stuffed Peppers with Butternut Squash and Quinoa

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These stuffed peppers with butternut squash, Great Northern Beans, and quinoa are a colorful and tasty meal for special events or every day. They are vegan and gluten-free. This is the perfect recipe for a distinctive main dish or side dish for a vegan holiday substitute for turkey, ham, etc. since they are delicious and filling. Plus, they are low in fat and heart-healthy with fiber and phytonutrients.

stuffed peppers with butternut squash and quinoa in a white baking dish topped with chopped parsley and basil leaves

Stuffed peppers with butternut squash are a great make-ahead dish for meal prep for the coming week. Beans and quinoa transform the classic recipe into a healthier main dish. A half of a stuffed pepper is a good-sized portion for lunch and would go well with fruit, a salad, or soup. Try it for a side dish with dinner, or perhaps have two halves for the main course.

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Key Ingredients

Bell peppers: I like the combination of red, orange, green, and yellow ones for a beautiful variety. The orange, red, and yellow peppers are sweeter and higher in vitamin C. Poblano peppers may be used instead of bell peppers.

Butternut Squash: Other types of winter squash like acorn, delicata, Hubbard, or kabocha could be used instead of butternut squash. The skin of delicata squash is very thin and is edible.

Quinoa: I chose quinoa instead of rice for more fiber and protein. I really like the look of tricolor quinoa, but white or red quinoa is fine to use too. Other nutritious options include farro, bulgur, and whole-wheat couscous.

Great Northern Beans or Other Protein Add-ins: Many stuffed pepper recipes call for cooked beef or turkey and cheese. I selected the Great Northern beans because they don’t overshadow the appearance of the squash. Cannelini or garbanzo beans are also light in color, but you could substitute for any other cooked beans, tofu, nuts, or seeds.

Crushed tomatoes: these help to hold the filling together and add flavor. I suggest looking for a reduced-sodium can of crushed tomatoes. Fresh chopped tomatoes would provide the flavor, but the stuffing ingredients won’t stay together well.

More ideas: You could add a frozen vegan meat substitute to this recipe. Shredded vegan cheese is an option, or you can sprinkle the top of the peppers with nutritional yeast for a cheesy flavor.

What is Quinoa?

Quinoa is a nutritious grain, with 6 grams of protein and 3 grams of fiber in a serving (1/4 cup uncooked). It is also gluten-free. When preparing quinoa, it is important to rinse it well first to prevent a soapy or bitter taste. You can buy white, red, black, or tricolor quinoa. They taste the same, but the darker ones look really dramatic!

quinoa being rinsed in colander
Rinsing Quinoa

Then, check the package for the cooking directions. The brand I purchased said to cook a cup of quinoa with 2 cups of water and a teaspoon of salt. Quinoa is so much fun to cook. It changes from little round particles to visible spirals in about 15 minutes. It really fluffs up to around 3 cups – more than you’ll need for this recipe.

I leave out the salt when cooking quinoa. One teaspoon is about 2,400 mg. of sodium: more than people should eat in one day. This seems unnecessary as other herbs and flavorings can be used to add taste in a healthier way, and I include a little salt in the recipe.

If you don’t have quinoa, you could use cooked wild or brown rice, farro, or bulgur instead.

How to Cook Butternut Squash

Slice the butternut squash in half, scoop out the seeds and brush on a little olive oil (your choice, it really doesn’t need it), and bake at 400 degrees F for 75 minutes. This recipe used just a quarter of the squash.

Sliced butternut squash
Sliced butternut squash

If you have an Instant Pot, cooking is very fast. Cut in half and scoop out the seeds, then place them on the steamer and add a cup of water to the inner liner. Cook for 8 minutes at high pressure. Allow 10 – 15 minutes for some natural pressure release. This was in a 6 quart Instant Pot Duo.

Here are ideas for cooking and flavoring acorn squash, which would be fine instead of butternut squash. Then I store the extra squash in the freezer to use in a variety of meals and soups.

You can also substitute butternut squash for the kabocha squash in this easy pasta recipe.

Winter squashes are good sources of beta-carotene, potassium, fiber, vitamin C, and magnesium (Source: Harvard School of Public Health).

How to Prepare Stuffed Peppers with Butternut Squash

I like to slice the peppers lengthwise. This makes it easier to cut out the seeds and ribs, and half of a stuffed pepper is a good size for a side dish. Then, bake them first to ensure they are soft enough after the stuffing is added and baked.

red, yellow, and bell pepper halves in blue dish
red, yellow, and bell pepper halves

Recipe Variations for Stuffed Peppers

You can use a variety of vegetables for this recipe. It’s a great way to use up extra cooked squash or whole grains.

  • Add a cup of raw baby spinach, kale, or diced zucchini when cooking the vegetables on the stovetop.
  • Top with 2 tablespoons of sliced olives, sunflower seeds, and/or chopped nuts.
  • Include 1/2 – 1 cup cooked beans, chickpeas, lentils, raw or frozen peas or corn (you may then wind up with some extra stuffing).

Preparation Notes

I have cooked these in the oven, but a slow cooker would be fine to use too. My estimate is 3 hours on high with some water in the bottom of the pot to prevent burning. If you try it, let me know how it works out.


These stuffed peppers with butternut squash can be stored in the refrigerator for 2-3 days, or in a covered container in the freezer for up to 3 months.

Do you have to cook the peppers first?

You don’t have to, but I prefer them on the softer side.

How do you cut a bell pepper?

I recommend using a paring knife and cutting them in half lengthwise. then, it is easy to cut around the stem. Seeds can get everywhere: just rinse out your pepper to easily get rid of them.

What kind of crushed tomatoes should I use?

Look for a reduced-sodium brand for a healthier option.

Related Recipes You May Enjoy

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stuffed peppers with butternut squash and quinoa in a white baking dish topped with chopped parsley and basil leaves

Stuffed Peppers with Butternut Squash and Quinoa

Melissa Altman-Traub MS, RDN, LDN
These Italian-style stuffed peppers with butternut squash, Great Northern beans, quinoa, and herbs are a great vegan meal for everyday, holidays, and entertaining. They freeze well, too.
5 from 13 votes
Prep Time 10 minutes
Cook Time 50 minutes
Total Time 1 hour
Course Main Course, Side Dish
Cuisine American, Italian
Servings 6
Calories 114 kcal


  • Large baking pan
  • Nonstick skillet
  • Cutting board
  • Chef's knife
  • paring knife


  • 3 bell peppers
  • 1 teaspoon light olive oil
  • ½ cup chopped onions
  • 1 teaspoon minced fresh garlic
  • ¼ cup tricolor quinoa
  • ¾ cup vegetable broth or water
  • ¾ cup cooked, chopped, and peeled butternut squash
  • 1 ⅓ cup cooked Great Northern beans
  • teaspoon salt
  • few turns fresh ground black pepper
  • ¼ teaspoon dried oregano
  • ¼ teaspoon dried basil
  • teaspoon dried rosemary
  • 3 ounces crushed tomatoes
  • 1 tablespoon chopped fresh parsley, basil, or both


  • Preheat the oven to 400° F. Spray a 9' x 13" baking pan with non-stick spray or spread with a little olive oil.
  • Slice the peppers in half lengthwise. Cut out the core and stem, and remove the seeds.
  • Arrange the peppers cut side up in the baking pan. Bake the peppers for 10 minutes.
  • While the peppers are baking, add the olive oil to a large non-stick skillet and place over medium heat. Cook the onions for 3 minutes, stirring occasionally. Add the garlic and cook for one more minute. Watch closely and stir if needed to prevent browning.
  • Rinse the quinoa well in a fine sieve and add it to the pan. Add the vegetable broth or water and stir. Cover the pan with a lid and turn the heat down to low. Cook for 15 minutes. Turn off the heat and leave the lid on for another 10 minutes. The quinoa should now be fluffy and have little spirals visible. If not, add a little more liquid, cover, and cook on low for a few more minutes.
  • Add the cooked butternut squash, beans, salt, pepper, oregano, basil, rosemary, and crushed tomatoes to the pan. Mix well.
  • Scoop about ½ cup of the mixture into each pepper half (an ice cream scoop makes this easy). Bake the stuffed peppers for 20 minutes. The peppers should be soft.
  • Remove the pan of peppers from the oven and top with chopped parsley and/or basil.


The nutrition estimate is from Spoonacular, which is based mainly on USDA data. Parsley was used for the fresh herbs.
Poblano peppers may be used instead of bell peppers.
Other types of winter squash like acorn or kabocha could be used instead of butternut.
You can use white or red quinoa too.
Feel free to substitute garbanzo bean, into beans, or other beans in this recipe.


Serving: 1half pepperCalories: 114kcalCarbohydrates: 21gProtein: 5gFat: 2gSaturated Fat: 0.3gPolyunsaturated Fat: 0.5gMonounsaturated Fat: 1gSodium: 190mgPotassium: 450mgFiber: 5gSugar: 4gVitamin A: 3876IUVitamin C: 84mgCalcium: 55mgIron: 2mg
Keyword Butternut Squash, Gluten-Free, Quinoa, Stuffed peppers, Vegan
Tried this recipe?Let us know how it was!

Wondering where to find more recipes? Here are some websites, blogs, and books I recommend: 15 Fantastic Sources for Vegetarian Recipes.

And check out warming winter bakes like Healthy Vegan Carrot Cake with Cashew Icing from

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How did you like these stuffed peppers with butternut squash? Please rate them and leave a comment below:

Originally published: 2/2/20. Updated 11/1/22

16 thoughts on “Stuffed Peppers with Butternut Squash and Quinoa”

  1. 5 stars
    Deliciously balanced and satisfying! The sweetness of butternut squash perfectly complements the hearty quinoa, while the stuffed peppers add a delightful touch of freshness. A must-try recipe for a wholesome and flavorful meal.

  2. 5 stars
    5 Star- I am looking forward to making this again as we roll into Fall. The flavors worked so well together. Great site

  3. 5 stars
    This dish is healthy and delicious. I never thought of stuffing peppers with roast squash. it’s very comforting and easy to make.

    1. Hi Mary. Thank you for pointing this out. it was a mistake and I removed them from the instructions. I just have the marinara sauce on top. However, I do think that chopped fresh tomatoes or canned tomatoes would go well and would use half of a cup if I included them in the stuffing mix.

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