This irresistible Spaghetti Squash Enchilada Bowls recipe is one of my favorite ways to enjoy spaghetti squash. It’s simple, satisfying, and made with just a handful of ingredients. These low-carb, oven-baked squash boats are perfect for weeknight dinners or meal prep, and they come together with minimal effort.

Spaghetti Squash Enchilada Bowls
If you roast a spaghetti squash and wonder what to top it with, enchilada sauce is a fantastic option. Using leftover homemade enchilada sauce or a high-quality jarred sauce turns roasted spaghetti squash into a flavorful, comforting meal. I often make extra enchilada sauce when I prepare chicken enchiladas, then freeze the remainder for quick dinners like these squash bowls. The homemade sauce makes a noticeable difference in flavor, but either option works.

These enchilada bowls are naturally filling even without meat, thanks to the squash and cheese. They’re an excellent choice for a meatless meal, but they also accept a variety of protein options if you want to boost the protein content. I recommend the oven method for roasting the squash rather than the microwave: the oven produces drier, firmer strands that hold up better when topped with sauce and cheese.
Spaghetti Squash Variations
- Ground meat: Top with seasoned ground beef or turkey for a heartier meal.
- Chicken: Add shredded rotisserie or leftover cooked chicken for extra protein.
- Vegetarian: Stir in canned black beans and corn, or add sautéed vegetables for a more filling meatless option.

More Spaghetti Squash Ideas
- Turkey Taco Spaghetti Squash Boats — swap enchilada sauce for taco-seasoned turkey.
- Spaghetti Squash with Meat Ragu — top roasted squash with a rich meat sauce.
- Baked Spaghetti Squash and Cheese — a simple, cheesy casserole-style dish.
- Spaghetti Squash with Bacon and Parmesan — smoky bacon and salty cheese for extra flavor.
- Instant Pot Spaghetti Squash and Meat Sauce — cook squash and ragu together for convenience.
Spaghetti Squash Enchilada Bowls
This easy, flavorful recipe uses roasted spaghetti squash as the base for enchilada-style bowls. With about five main ingredients and simple steps, it’s a great low-carb weeknight dinner or meal-prep option.
Cals: 183 | Protein: 10 g | Carbs: 18.5 g | Fat: 10 g
Course: Dinner | Cuisine: American-inspired
Prep: 5 mins | Cook: 1 hr | Total: 1 hr 5 mins
Yield: 4 servings | Serving Size: 1 bowl
Ingredients
- 2 small spaghetti squashes
- 2 teaspoons olive oil
- 1/8 teaspoon kosher salt, plus more to taste
- Black pepper, to taste
- 1 1/3 cups enchilada sauce (homemade or store-bought)
- 1 cup part-skim shredded Mexican cheese blend
- Chopped cilantro and scallions for garnish
Instructions
- Preheat the oven to 400°F (200°C).
- Line a baking sheet with parchment paper. Cut each spaghetti squash in half lengthwise and scoop out the seeds and fibrous center.
- Brush the cut sides of the squash with olive oil and season lightly with salt and pepper. Place the squash halves cut side down on the baking sheet.
- Bake for 45–50 minutes, or until the flesh is tender and easily pierced with a fork. Oven times vary by squash size; larger squashes may need more time.
- Allow the squash to cool enough to handle. Use a fork to scrape and loosen the strands so they resemble spaghetti.
- Spoon enchilada sauce evenly into each squash bowl until nearly full.
- Top each bowl with shredded cheese. Return the filled squash halves to the oven and bake an additional 12–15 minutes until the cheese is melted and the filling is heated through.
- Remove from the oven, sprinkle with chopped cilantro and scallions, and serve immediately.

Notes & Tips
Roasting the squash in the oven produces a firmer texture and less moisture than microwaving, which helps the enchilada sauce cling to the strands. If you prefer a quicker method, you can microwave halved squash face-down for about 10–12 minutes depending on size, but expect a softer, wetter texture.
For added protein, stir in cooked shredded chicken, taco-seasoned ground turkey, or beans before topping with cheese. To make these dairy-free, use a dairy-free cheese substitute or skip the cheese and finish with extra herbs and a squeeze of lime.
Leftovers keep well in the refrigerator for 3–4 days. Reheat in the oven or a toaster oven to help the squash regain some of its firmness and to melt the cheese again.
Nutrition
Serving: 1 bowl — Calories: 183 kcal; Carbohydrates: 18.5 g; Protein: 10 g; Fat: 10 g; Saturated Fat: 0.5 g; Cholesterol: 15 mg; Sodium: 790 mg; Fiber: 3.5 g; Sugar: 6 g.
Final Thought
If you try this Spaghetti Squash Enchilada Bowls recipe, note any tweaks you make and enjoy experimenting with different proteins and toppings. It’s an easy, flavorful way to turn roasted spaghetti squash into a satisfying, low-carb meal.
