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These spaghetti squash enchilada bowls are a healthy twist on classic enchiladas! This easy vegetarian dinner is made with roasted spaghetti squash, enchilada sauce, beans, and cheese, and is naturally low-carb and high in fiber.

We love this recipe when we want all the bold enchilada flavors without the heaviness. It is simple to make, easy to customize, and perfect for busy weeknights or meal prep. It’s one of those dinners that feels comforting but still light and nourishing.
If you love the flavors of enchiladas, try our ground turkey enchilada skillet, slow cooker enchilada bowl, vegetarian cottage cheese enchilada bowl, classic chicken and cheese enchiladas, and enchilada egg skillet next!
Table of Contents
Why You Will Love These Spaghetti Squash Enchilada Boats
- Healthy: It’s a healthy, low-carb, high-fiber, gluten-free meal that is filling and satisfying.
- Lighter: These spaghetti squash enchilada bowls are lighter than traditional enchiladas but still have all the delicious flavors you love.
- Easy: They are easy to make. Simply roast the spaghetti squash, then add the enchilada sauce and your favorite toppings.
- Vegetarian: These enchilada bowls are naturally vegetarian. For another vegetarian option, try our cottage cheese enchilada bowls!
- Great for Meal Prep: This recipe is perfect for an easy weeknight meal and great for meal prep!
Ingredients Needed

- Spaghetti Squash: You’ll need one medium spaghetti squash for this recipe.
- Olive Oil Spray: Lightly spray the spaghetti squash halves with olive oil before seasoning and roasting. We love this oil sprayer.
- Salt & Pepper: Season the spaghetti squash with salt and pepper before roasting.
- Enchilada Sauce: Use your favorite can of red enchilada sauce.
- Black Beans: Rinsed and drained black beans add protein, fiber, and flavor.
- Cheese: Add light shredded cheddar cheese or light Mexican cheese blend for cheesy goodness.
- Green Onions & Cilantro: Top with sliced green onions and fresh chopped cilantro.
Find the full measurements in the recipe card below.
Substitutions & Variations
- High-Protein Option: You can make this recipe higher in protein by adding fully cooked shredded rotisserie chicken, our slow-cooker shredded chicken, or fully cooked ground turkey.
- Optional Add-Ins: Add corn, sautéed onions, or other vegetables for even more flavor.
- Enchilada Sauce Swap: Use your favorite red enchilada sauce, or swap it with green enchilada sauce for a different flavor.
- Cheese Options: Use light shredded cheddar cheese or a light Mexican cheese blend.
- Bean Options: You can add more black beans or swap in pinto beans if you prefer.
How To Make Spaghetti Squash Enchilada Bowls
Step 1: Carefully cut the spaghetti squash in half lengthwise and use a spoon to scrape out the seeds.

Step 2: Line a baking sheet with parchment paper. Lightly spray with olive oil and season with salt and pepper. Place the squash cut side down on the baking sheet and bake at 400°F for 45 to 50 minutes, or until tender.

Step 3: Once done, let the squash cool slightly. Use a fork to scrape the squash into strands, leaving it in the squash shells.
Step 4: Spoon the enchilada sauce mixture into each squash bowl until almost full. Mix in the black beans.

Step 5: Top evenly with the cheese, then return the squash to the oven and bake for another 10-15 minutes, until the cheese is melted and the sauce is heated through.

Step 6: Remove from the oven, sprinkle with green onions and cilantro, and serve.
Serving Suggestions
Serve these spaghetti squash enchilada bowls as is, or with your favorite toppings. You can add sliced olives or jalapeños for extra flavor and heat, and finish them with a dollop of Greek yogurt or light sour cream if desired. Or, add a dollop of our cottage cheese queso or top with crushed tortilla chips for crunch.
We love to serve these with cilantro lime cauliflower rice, Spanish cauliflower rice, Mexican street corn dip, crispy air fryer potatoes, healthy guacamole, or homemade Pico de Gallo for a delicious meal.
Expert Tips
- Strands: Gently scrape the squash with a fork to create strands while keeping the shells intact. Or, you can scrape the strands into a bowl, add the toppings, and serve it that way if you prefer.
- Cool Slightly: Let the spaghetti squash cool slightly before scraping the strands so it’s easier to handle.
- Don’t Burn the Cheese: Keep an eye on the spaghetti squash while the cheese melts so it doesn’t burn.
Storage Instructions
You can store leftover spaghetti squash enchilada bowls in an airtight container in the refrigerator for 2-3 days.
Frequently Asked Questions
Can I Make Spaghetti Squash Enchilada Bowls Ahead of Time?
Yes, simply roast the spaghetti squash ahead of time and store the strands in an airtight container in the refrigerator. When ready to serve, add the enchilada sauce, beans, and cheese, then bake until heated through.
Are Spaghetti Squash Enchilada Bowls Vegetarian?
As written, these spaghetti squash enchilada bowls are vegetarian. They are made with spaghetti squash, black beans, enchilada sauce, and cheese.
More Spaghetti Squash Recipes!
- Mediterranean Spaghetti Squash
- Chicken Alfredo Spaghetti Squash
- Marry Me Chicken Spaghetti Squash
- Garlic Parmesan Spaghetti Squash
- Air Fryer Spaghetti Squash
- Slow Cooker Spaghetti Squash
If you try this recipe, please be sure to leave us a comment and star rating, ★★★★★, letting us know how it turns out for you.
Spaghetti Squash Enchilada Bowls

Ingredients
- 1 medium spaghetti squash
- olive oil spray
- 1/4 teaspoon salt
- 1/8 teaspoon pepper
- 1, 15.5-ounce can of red enchilada sauce
- 1/2 cup black beans, rinsed and drained
- 3/4 cup light shredded cheddar cheese or light Mexican cheese blend
- 2 green onions, sliced
- 2 tablespoons fresh cilantro, chopped
Instructions
- Carefully cut the spaghetti squash in half lengthwise and use a spoon to scrape out the seeds.
- Line a baking sheet with parchment paper. Lightly spray with olive oil and season with salt and pepper. Place the squash cut side down on the baking sheet and bake at 400°F for 45 to 50 minutes, or until tender.
- Once done, let the squash cool slightly. Use a fork to scrape the squash into strands, leaving it in the squash shells.
- Spoon the enchilada sauce mixture into each squash bowl until almost full. Mix in the black beans.
- Top evenly with the cheese, then return the squash to the oven and bake for another 10-15 minutes, until the cheese is melted and the sauce is heated through.
- Remove from the oven, sprinkle with green onions and cilantro, and serve.
Video

Notes
- Bean Options: You can add more black beans or swap in pinto beans if you prefer.
- High-Protein Option: You can make this recipe higher in protein by adding fully cooked shredded rotisserie chicken, our slow-cooker shredded chicken, or fully cooked ground turkey.
- Optional Add-Ins: Add corn, sautéed onions, or other vegetables for even more flavor.
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.















