Comfort Food

Gluten-Free Black Bean Enchilada Cups

Gluten-Free Black Bean Enchilada Cups

These gluten-free and vegetarian mini enchilada cups are packed with protein. Serve them as a healthy appetizer at your next party.

The trick to making this recipe is to bake the tortilla cups prior to filling them with the beans mix. This baking step yielded crispier shells that holds the filling well without falling apart. Baking the tortillas before and after with the filling leads to a perfectly shaped enchilada cup!

In addition to making the enchiladas, the second part of this recipe includes making a sauce. I had never made enchilada sauce before and always used salsa or tomato sauce for my enchiladas at home. This homemade version is not a perfect enchilada sauce, but it was easy and paired nicely with the enchilada cups. I was inspired by Cookie and Kate’s recipe. For the sauce, the main components are tomato paste, vegetable broth, gluten-free flour, and a mix of spices. If you prefer not to do extra cooking, feel free to pour salsa on top.

I used two cans of beans instead of meat. If you prefer meat or a meat alternative, substitute one can of beans for a pound of meat or alternative. Make sure to cook the meat thoroughly and set aside before cooking the onions and peppers. Add it back to the filling after separately cooking the vegetables and beans.

In addition to the beans and vegetables, add a mixed greens salad or any other non-starchy vegetable as a side dish to make a balanced meal. These enchilada cups can last up to three days in the refrigerator. If you choose to freeze them, keep them for no longer than three months.

These enchilada cups can get messy, but I promise no one will notice since everyone will be enjoying them!

Gluten-Free Black Bean Enchilada Cups

Prep Time: 10 minutes
Cook Time: 20 minutes
Total Time: 30 minutes
Yield: 12 tortilla cups
Serving Size: 2 to 3 tortilla cups


  • 12 small gluten free corn tortillas
  • 1 tablespoon olive oil
  • 1 medium pepper, diced
  • 1 small onion (or 1/2 large onion), diced
  • 2-3 cloves garlic, minced
  • 2 teaspoons ground cumin
  • 1/2 teaspoon cayenne pepper
  • 1/2 teaspoon chili powder
  • 1 15oz can low sodium black beans
  • 1 15 oz can low sodium red beans*
  • 1-1 1/2 cups cooked brown rice, optional
  • 1/4 cup shredded part skim cheese for topping, optional
  • Salsa or Enchilada Sauce* for topping, optional

Enchilada Sauce:

  • 1 tablespoon olive oil
  • 1/4 teaspoon garlic powder
  • 2 teaspoons dried basil
  • 1 teaspoon chili powder
  • 1 teaspoon paprika
  • 3 tablespoons gluten-free flour
  • 2 tablespoons tomato paste
  • 2 cups vegetable broth


  1. Preheat oven to 350 degrees F. Gently fold tortillas into lightly greased (or non-stick) muffin pan. Bake tortillas until crispy, about 5-8 minutes. Set aside.
  2. While the tortillas bake, heat olive oil on medium high heat in a skillet or non-stick pan. Saute onions and peppers until tender, about 5 minutes stirring frequently. Add the spices and garlic and cook for 1 minute. Then add the beans and cook for an additional minute, remove from heat, and set aside.
  3. Scoop the rice and fill the bottom of the tortilla cups. Next layer with the filling to the the top. (If preferred, mix the rice with the filling prior to placing separately in the tortilla cups).
  4. Place the filled tortilla cups in the oven and bake for 10-12 minutes to melt the cheese.
  5. Top with Enchilada Sauce (below) or salsa.
  6. Additional toppings: Scallions, sliced avocado, low fat sour cream
  7. Enchilada Sauce: In a non-stick pan or skillet, heat olive oil on medium high heat. Saute the spices, herbs, and flour for 1 minute.
  8. Add in the tomato paste and vegetable broth, stir with a whisk. Simmer for 5-7 minutes until sauce thickens. Remove from heat. Drizzle over enchilada cups.

Notes: *If you prefer adding meat (or meat alternative), substitute 1 can of beans for 1 lb of meat or meat alternative.

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