Fajita Stuffed Zucchini with Pinto Beans

Fajita Stuffed Zucchini with Pinto Beans are a light and healthy vegetarian meal packed with beans, fresh veggies, fajita seasoning, and cheese. Jump to Recipe


These Zucchini Boats stuffed with pinto beans, peppers, onions, and fajita seasoning and covered in melted cheese are the perfect vegetarian meal. Make a big batch and enjoy them all week long.  Vegetarians will also love these Roasted Vegetable Fajitas and Eggplant Fajitas.

This weekend we had a number of events and I definitely took advantage and enjoyed all the delicious treats. I definitely went overboard on the cheese, crackers, birthday cake, and wine. It was lovely but I am definitely feeling it today. To get back on track and reenergize my body, this week I am trying to pack in as many veggies as possible.

Since a girl can only eat so many salads, these Fajita Stuffed Zucchini with Pinto Beans are the perfect alternative. Stuffed with pinto beans, peppers, red onion, and lots of spices – you get all the flavor of fajitas packed into a perfect little zucchini boat. Honestly, zucchini boats are one of my favorite veggie-centered meals and there are so many good options – Zucchini and Ground Turkey Pizza BoatsTurkey Fajita Zucchini BoatsChicken Parmesan Zucchini Boats, and classic Zucchini Pizza Boats.

Pinto beans, peppers, onions, and fajita seasoning cooking in a skillet for zucchini boats.

Main Ingredients and Easy Swaps

  • Zucchini: Zucchini is the perfect vehicle for making these stuffed vegetable boats but you could also use yellow squash, eggplant, butternut squash (cooked longer), or even cucumbers, just don’t bake them. 
  • Pinto beans: Any beans you like will work including pinto beans, black beans, chickpeas, kidney beans, or white beans.
  • Peppers and onions: Since this recipe is inspired by fajitas, peppers and onions are the perfect filling. Any bell peppers or onions will work. For more spice, use a poblano pepper or jalapeno pepper as well.
  • Fajita seasoning: Fajita seasoning is a combination of cumin, chili powder, garlic powder, onion powder, paprika, and more. You can make your own homemade fajita seasoning, use store-bought, or swap in taco seasoning.
  • Mozzarella cheese: Use any cheese that melts well for these zucchini boats including mozzarella, cheddar, pepper jack, or Monterey Jack. 

Recipe Ideas and Tips

There are so many different ways to customize this recipe and make it your own. Here are some ideas:

  • Make this dish spicy by swapping in jalapeno or poblano peppers for some of the bell peppers.
  • Add some fresh baby spinach and zucchini to the skillet with peppers and onions for even more veggie goodness.
  • Add protein with some ground turkey, ground beef, or vegetarian crumbles.
  • Top the finished dish with some homemade jalapeno ranch or pico de gallo.
  • Add extra moisture to the dish by adding a can of drained fire-roasted tomatoes to the peppers and onions.
  • Top the finished product with some sour cream, plain Greek yogurt, or creme fraiche.

How to make zucchini boats?

The easiest way to make the zucchini boats is to simply scoop out the middle of the zucchini with a spoon. Basically, you want to scoop out the seeds and soft part of the zucchini. Then either discard that part of chop it up and saute it with the peppers and onions. 

Pinto bean zucchini boats with peppers, onions, fajita seasoning, and melted cheese on a baking sheet.

Storage and Leftovers

This dish is great for meal prep since it is easy to reheat and stays fresh in the fridge for up to 4-5 days. It can also be frozen. Let the zucchini boats fully cool and then wrap them individually before placing them in the freezer for up to 3 months.

Frequently Asked Questions

Here are some of the most common questions people have about making these zucchini boats. 

Can these be made with ground beef or turkey to add more protein?

Absoltuely1 Just brown the ground meat in the pan so it is fully cooked and fold it into the bean and vegetable mixture. Plan on adding extra zucchini if you add ground beef since you will have more of the filling. 

Do you eat the skin on zucchini boats?

Zucchini skin is tender and tastes the same as the rest of the zucchini. It can be eaten and has a very mild flavor. I

How do I make sure the zucchini is fully cooked?

This recipe cooks for 25 minutes, which ensures that a small or medium-sized zucchini will cook through. If you prefer the zucchini very soft, wrap the pan in aluminum foil while it bakes. Remove the foil in the last few minutes for the cheese to lightly brown. 

Can I make boats with different vegetables?

This bean and vegetable fajita filling will work with lots of different vegetables including summer squash, eggplant, butternut squash, acorn squash, or bell peppers. You can also use it in lettuce wraps, crunchy cucumber boats, or serve it over cauliflower rice.

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