Spaghetti Squash Enchilada Casserole is a delicious, low-carb twist on classic enchiladas, packed with bold Mexican flavors and wholesome ingredients. This casserole replaces traditional tortillas with nutrient-rich spaghetti squash, making it a gluten-free, keto-friendly, and high-fiber alternative to the classic dish. It’s perfect for anyone looking to enjoy a comforting meal without the extra carbs.
In this article, you’ll learn how to make the perfect Spaghetti Squash Enchilada Casserole, including ingredient swaps, cooking techniques, and tips for avoiding a watery casserole. Plus, we’ll answer common questions like how to prevent sogginess, whether spaghetti squash is anti-inflammatory, and the best way to store leftovers.
Why You’ll Love This Recipe
- Healthy & Low-Carb – Packed with fiber, protein, and essential nutrients.
- Versatile – Easily adaptable for vegetarian, vegan, and keto diets.
- Meal-Prep Friendly – Stores, reheats, and freezes well for easy meals.
- Bold & Cheesy Flavor – Comfort food without the guilt.
Ingredients & Substitutions
A great Spaghetti Squash Enchilada Casserole starts with the right ingredients. This dish is naturally gluten-free, low-carb, and packed with nutrients, making it an excellent choice for a healthier enchilada alternative. Whether you want a classic Spaghetti Squash Enchilada Casserole or a vegan-friendly variation, there are plenty of ways to customize it.
Essential Ingredients for the Best Spaghetti Squash Enchilada Casserole
To make the perfect Spaghetti Squash Enchilada Casserole, you’ll need:
- Spaghetti Squash – The star ingredient that gives the casserole a noodle-like texture while keeping it low-carb.
- Shredded Chicken or Black Beans – Choose between shredded chicken for protein or black beans for a vegetarian option.
- Enchilada Sauce – A rich and flavorful sauce that defines the classic enchilada taste. Red, green, or homemade enchilada sauce all work great.
- Bell Peppers & Onions – These vegetables add natural sweetness and texture to your Spaghetti Squash Enchilada Casserole.
- Cheese – A Mexican cheese blend, cheddar, or Monterey Jack gives that classic enchilada casserole texture. Use dairy-free cheese for a vegan-friendly version.
- Spices – Chili powder, cumin, smoked paprika, and garlic powder enhance the flavors.
- Cilantro & Lime – Fresh garnishes that bring out the zesty and bold taste of this casserole.
Best Ingredient Substitutions for Spaghetti Squash Enchilada Casserole
1. Protein Options for Spaghetti Squash Enchilada Casserole
- Chicken substitute: Black beans, pinto beans, lentils, tofu, or tempeh
- Ground turkey or beef substitute: Vegan crumbles, jackfruit, or mushrooms
2. Dairy-Free or Vegan Alternatives
- Cheese substitute: Dairy-free shredded cheese, nutritional yeast, or cashew-based queso
- Sour cream topping alternative: Cashew cream, dairy-free yogurt, or guacamole
3. Enchilada Sauce Options
- Mild Flavor: Green enchilada sauce or a homemade tomato-based sauce
- Spicy Kick: Add chipotle peppers or hot sauce to your enchilada sauce
- Low-Sodium: Make a homemade sauce to control salt levels
By choosing the right ingredients, you can customize your Spaghetti Squash Enchilada Casserole to match your flavor and dietary preferences.
Step-by-Step Cooking Instructions
Making a Spaghetti Squash Enchilada Casserole is simple, but the key to getting the perfect texture and flavor lies in the preparation. Follow these steps to ensure your casserole is flavorful, cheesy, and never watery or mushy.
1: Prepare the Spaghetti Squash
Properly cooking spaghetti squash is crucial to avoid a watery Spaghetti Squash Enchilada Casserole. Follow these methods for the best results:
Oven-Roasting (Best for Flavor & Texture)
- Preheat your oven to 400°F (200°C).
- Cut the spaghetti squash in half lengthwise and scoop out the seeds.
- Drizzle with olive oil, sprinkle with salt and pepper, and place the halves cut-side down on a baking sheet.
- Roast for 35-40 minutes until the flesh is tender and easily shredded.
- Let the squash cool slightly, then use a fork to shred it into spaghetti-like strands.
Pro Tip: To remove excess moisture, place the shredded squash in a clean kitchen towel and squeeze out extra liquid before adding it to the casserole.
Microwave Method (Faster, but More Moisture Retention)
- Poke holes in the squash with a fork and microwave for 5-7 minutes to soften.
- Carefully cut in half, scoop out the seeds, and microwave again for another 5 minutes until soft.
- Shred into strands using a fork and drain excess moisture before using.
2: Cook the Enchilada Filling
While the spaghetti squash is cooking, prepare the flavorful enchilada filling:
- Heat 1 tablespoon of olive oil in a large skillet over medium heat.
- Sauté diced onions and bell peppers for about 3-4 minutes until softened.
- Add shredded chicken or black beans, stirring to combine.
- Pour in 1 cup of enchilada sauce and season with chili powder, cumin, and smoked paprika.
- Simmer for 5 minutes, stirring occasionally, until everything is well coated and heated through.
Want more spice? Add chopped jalapeños or a dash of hot sauce!
3: Assemble the Spaghetti Squash Enchilada Casserole
Now it’s time to bring everything together:
- Preheat the oven to 375°F (190°C).
- Layer half of the shredded spaghetti squash at the bottom of a greased baking dish.
- Spread half of the enchilada filling evenly over the squash.
- Sprinkle half of the cheese on top for a gooey, melty texture.
- Repeat the layers with the remaining squash, filling, and cheese.
- Drizzle extra enchilada sauce over the top for added flavor.
4: Bake Until Golden & Bubbly
- Cover the dish with foil and bake for 20 minutes.
- Remove the foil and bake for another 10 minutes until the cheese is melted and slightly golden.
- Let the casserole rest for 5 minutes before serving.
Want extra crisp? Broil the casserole for 2-3 minutes at the end for a golden, bubbly cheese topping.
5: Garnish & Serve
Once your Spaghetti Squash Enchilada Casserole is out of the oven, finish with:
✔ Fresh cilantro
✔ Sliced avocado
✔ A squeeze of lime
✔ Dollop of sour cream or Greek yogurt
Now you’re ready to enjoy a cheesy, comforting, and nutritious enchilada casserole that’s packed with flavor!
Love casseroles? Don’t miss our Green Bean Casserole Recipe—a holiday favorite with a crispy, golden topping!
Tips for the Perfect Texture (Avoiding Sogginess)
One of the biggest challenges when making a Spaghetti Squash Enchilada Casserole is keeping it from becoming too watery or mushy. Since spaghetti squash naturally holds a lot of moisture, improper preparation can result in a soggy casserole. Here are some pro tips to keep your dish firm, flavorful, and perfectly textured.
1. What Is the Secret to Non-Soggy Enchiladas?
A common issue with enchiladas and casseroles is excess moisture. Here’s how to prevent a watery mess:
✔ Drain the spaghetti squash properly – After roasting or microwaving, place the squash strands in a clean kitchen towel and squeeze out extra liquid before layering.
✔ Use a thick enchilada sauce – Avoid watery sauces; opt for homemade or thicker store-bought options. If needed, simmer the sauce for a few minutes to reduce excess liquid.
✔ Shred cheese fresh – Pre-packaged shredded cheese contains anti-caking agents that add moisture. Grate cheese fresh for better melting and texture.
✔ Bake uncovered for the last 10 minutes – This helps evaporate any remaining moisture, keeping the casserole firm.
2. Why Did My Spaghetti Squash Get Mushy?
If your spaghetti squash is too soft, it may have been overcooked or not drained properly. Here’s how to fix it:
✔ Roast instead of steaming – Steaming or microwaving holds more moisture. Roasting at 400°F for 35-40 minutes dries it out better.
✔ Cut baking time if necessary – If your squash is extra large, check at 30 minutes to avoid over-roasting.
✔ Let it cool before shredding – Hot spaghetti squash releases more water when shredded immediately. Let it rest 5-10 minutes before using.
3. How Do You Keep Squash Casserole from Getting Watery?
Excess liquid in casseroles comes from both the squash and added ingredients. Here’s how to prevent it:
✔ Pre-cook vegetables – Bell peppers, onions, and mushrooms release moisture when baked. Sauté them first before adding them to the casserole.
✔ Drain beans and cooked proteins – If using beans or shredded chicken, pat them dry before mixing to avoid extra liquid.
✔ Layer smartly – Start with a thin layer of spaghetti squash at the bottom, followed by filling and cheese to create a structure that doesn’t get soggy.
4. The Final Trick: Let It Rest Before Serving
Once baked, let your Spaghetti Squash Enchilada Casserole sit for 5-10 minutes before slicing. This helps the layers set and absorb any remaining moisture, making each bite firm and flavorful.
By following these simple steps, your casserole will have the perfect cheesy, slightly crispy top while staying moist but not watery.
Looking for another creamy, flavorful dish? Check out this Green Spaghetti Recipe—a vibrant, cheesy pasta that’s just as comforting!
Health Benefits of Spaghetti Squash Enchilada Casserole
Not only is Spaghetti Squash Enchilada Casserole delicious and comforting, but it also comes with several health benefits. By swapping out traditional tortillas for spaghetti squash, you’re creating a low-carb, fiber-rich, and nutrient-packed meal that supports overall wellness.
1. Is Spaghetti Squash an Anti-Inflammatory Food?
Yes! Spaghetti squash is naturally anti-inflammatory due to its high antioxidant content and low carbohydrate profile. Here’s why:
✔ Rich in Vitamin C – Supports the immune system and helps fight inflammation.
✔ Loaded with Beta-Carotene – A powerful antioxidant that promotes skin health and reduces oxidative stress.
✔ Low in Sugar – Unlike regular pasta or tortillas, spaghetti squash has a low glycemic index, meaning it won’t spike blood sugar levels.
✔ Packed with Fiber – Helps with digestion, promotes gut health, and reduces inflammation in the digestive tract.
By using spaghetti squash instead of traditional tortillas, you’re not only reducing empty carbs but also supporting your body’s natural anti-inflammatory processes.
2. Low-Carb & Keto-Friendly Benefits
A single cup of cooked spaghetti squash contains only about 7 grams of carbs, making it a fantastic alternative to high-carb tortillas or rice. This is why Spaghetti Squash Enchilada Casserole is popular among those following low-carb, keto, or paleo diets.
✔ Supports weight loss – The high fiber content keeps you full longer without excessive calories.
✔ Helps regulate blood sugar – Low glycemic foods like spaghetti squash prevent insulin spikes.
✔ Provides essential nutrients – Unlike processed tortillas, spaghetti squash delivers vitamins and minerals with fewer calories.
3. High in Fiber for Digestive & Gut Health
Fiber plays a crucial role in digestion, and Spaghetti Squash Enchilada Casserole is an excellent source of it. The combination of spaghetti squash, beans (if using), and vegetables helps:
✔ Promote healthy digestion and prevent bloating
✔ Support gut-friendly bacteria for better overall gut health
✔ Reduce cholesterol levels and support heart health
4. Protein-Packed for Muscle & Energy
Adding chicken, turkey, or beans to this Spaghetti Squash Enchilada Casserole boosts its protein content, making it a well-rounded, muscle-supporting meal. Protein is essential for:
✔ Building and repairing muscles
✔ Providing long-lasting energy
✔ Keeping you full and satisfied
If you’re following a vegetarian or vegan diet, you can still make this casserole protein-rich by using:
✔ Black beans, pinto beans, or lentils
✔ Tofu or tempeh
✔ Dairy-free cheese alternatives with protein
5. Gluten-Free & Dairy-Free Adaptability
Traditional enchiladas contain flour tortillas and heavy cheese, making them unsuitable for those with gluten or dairy sensitivities. However, this Spaghetti Squash Enchilada Casserole is naturally gluten-free, and with a few swaps, it can also be made dairy-free:
✔ Use dairy-free cheese alternatives like nutritional yeast or cashew-based queso
✔ Opt for a plant-based enchilada sauce (check labels for gluten)
✔ Top with avocado or dairy-free sour cream for extra creaminess
Customizing Your Enchilada Casserole
One of the best things about Spaghetti Squash Enchilada Casserole is its versatility. Whether you’re looking for a vegetarian, vegan, high-protein, or spicier version, this recipe can be easily adjusted to match your dietary preferences. Below are some of the best ways to customize this dish to fit your needs.
1. Vegetarian & Vegan Variations
If you want a meatless Spaghetti Squash Enchilada Casserole, simply swap out the protein for a plant-based option. Here’s how to keep it flavorful and satisfying:
✔ Use black beans, pinto beans, or lentils instead of shredded chicken or ground turkey
✔ Add extra vegetables like mushrooms, zucchini, or spinach for texture and nutrients
✔ Replace cheese with dairy-free options like cashew queso, nutritional yeast, or vegan shredded cheese
Pro Tip: A cashew-based sour cream or avocado crema makes a delicious dairy-free topping!
2. High-Protein Additions
For those looking to increase protein intake, here are some ways to make this Spaghetti Squash Enchilada Casserole even more satisfying:
✔ Shredded chicken or turkey – Lean, protein-packed, and easy to season
✔ Ground beef or turkey – Adds richness and a hearty texture
✔ Tofu or tempeh – A great plant-based protein alternative
✔ Greek yogurt or cottage cheese – Mix into the sauce for added creaminess and protein boost
Want even more protein? Sprinkle hemp seeds or shredded chicken on top before serving!
3. Adjusting the Spice Level
If you love bold, spicy flavors, here are a few ways to amp up the heat:
✔ Use a spicy enchilada sauce (chipotle, red chili, or fire-roasted flavors)
✔ Add diced jalapeños or serrano peppers to the filling
✔ Sprinkle in extra cayenne pepper or crushed red pepper flakes
✔ Drizzle hot sauce on top before serving
For a milder version, use a green enchilada sauce and reduce or omit the spicy seasonings.
4. Making It Dairy-Free or Keto-Friendly
✔ Dairy-Free: Swap regular cheese for dairy-free shredded cheese, nutritional yeast, or cashew queso
✔ Keto-Friendly: Stick to low-carb ingredients (avoid beans) and use full-fat cheese for extra creaminess
5. Fun Flavor Twists & Toppings
Want to elevate your Spaghetti Squash Enchilada Casserole? Try these tasty upgrades:
✔ Roasted corn & black bean topping – Adds a smoky, Southwest-style flair
✔ Crushed tortilla chips – Sprinkle on top for a crunchy texture (not keto-friendly)
✔ Avocado slices or guacamole – For creaminess and a boost of healthy fats
✔ Sour cream or Greek yogurt – Adds richness while balancing spice
✔ Cilantro & lime juice – Brightens up every bite
Serving & Pairing Suggestions
A delicious Spaghetti Squash Enchilada Casserole deserves the perfect sides and drinks to complement its flavors. Whether you’re serving this dish for a weeknight dinner or a gathering, here are the best pairings, toppings, and beverages to enhance your meal.
1. What to Serve with Spaghetti Squash Enchilada Casserole
Since this casserole is packed with bold enchilada flavors, it pairs well with fresh, crunchy, and creamy sides.
✔ Mexican Coleslaw – A tangy slaw made with cabbage, lime juice, and cilantro balances the richness of the casserole.
✔ Guacamole & Chips – Creamy guacamole with crunchy tortilla chips makes a great appetizer or side.
✔ Black Beans & Rice – If you’re not following a low-carb diet, classic Mexican-style black beans and rice add a hearty element.
✔ Grilled Vegetables – Bell peppers, zucchini, and mushrooms complement the smoky flavors in the casserole.
✔ Corn Salsa – A sweet and spicy corn salsa with tomatoes, red onion, and jalapeños brightens up the meal.
Looking for a low-carb side? Try a cucumber-tomato salad with lime dressing!
2. Best Toppings for Extra Flavor
✔ Sliced Avocado or Guacamole – Adds creamy, healthy fats
✔ Fresh Cilantro – Brings a burst of fresh, herby flavor
✔ Crumbled Cotija or Feta Cheese – Enhances the cheesy texture
✔ Sour Cream or Greek Yogurt – Balances the spice with cool creaminess
✔ Lime Wedges – A squeeze of lime juice brightens up every bite
✔ Pickled Jalapeños – For a spicy, tangy kick
Want more crunch? Sprinkle crushed tortilla chips or pumpkin seeds on top!
3. Best Drinks to Pair with This Casserole
A Spaghetti Squash Enchilada Casserole pairs well with both refreshing and bold drinks. Here are some top picks:
Non-Alcoholic Pairings
✔ Agua Fresca – A light fruit-infused water (like watermelon, cucumber-lime, or hibiscus)
✔ Iced Tea with Lemon – A refreshing, slightly sweet pairing
✔ Sparkling Water with Lime – Keeps it light and bubbly
✔ Horchata – A creamy cinnamon rice milk that complements the spice
Alcoholic Pairings
✔ Margaritas – Classic lime margaritas (or a spicy jalapeño version) work beautifully
✔ Light Mexican Beer – Like Corona, Modelo, or Pacifico with a squeeze of lime
✔ Sangria – A fruity red or white sangria complements the smoky, cheesy flavors
✔ Tequila Paloma – A grapefruit-based cocktail that adds citrusy freshness
FAQs – Answering Common Questions
Before you make your Spaghetti Squash Enchilada Casserole, you may have a few questions about getting the perfect texture, flavor, and consistency. Below are answers to some of the most commonly asked questions.
1. What Is the Secret to Non-Soggy Enchiladas?
The key to non-soggy enchiladas or casseroles is to control excess moisture. Here’s how:
✔ Drain spaghetti squash properly – After cooking, place the strands in a clean kitchen towel and squeeze out extra liquid.
✔ Use a thicker enchilada sauce – If your sauce is too thin, simmer it for a few minutes before adding it to the casserole.
✔ Pre-cook your vegetables – Bell peppers, onions, and mushrooms release moisture when baked. Sauté them first to avoid extra liquid.
✔ Bake uncovered for the last 10 minutes – This helps evaporate any remaining moisture, keeping the casserole firm.
2. Is Spaghetti Squash an Anti-Inflammatory Food?
Yes! Spaghetti squash is naturally anti-inflammatory due to its high antioxidant and fiber content. It contains:
✔ Vitamin C & Beta-Carotene – Help reduce inflammation and support the immune system.
✔ Low-Carb & Low-Sugar – Unlike tortillas, spaghetti squash has a low glycemic index, which means it won’t spike blood sugar.
✔ Gut-Healthy Fiber – Supports digestion and reduces bloating.
By swapping traditional tortillas for spaghetti squash, you’re making a healthier, anti-inflammatory meal.
3. How Do You Keep Squash Casserole from Getting Watery?
To avoid a watery casserole, follow these steps:
✔ Roast spaghetti squash instead of steaming or microwaving – Roasting removes moisture, while steaming adds more.
✔ Let it cool before shredding – Hot spaghetti squash releases extra water. Wait 5-10 minutes before shredding.
✔ Drain any excess liquid – Use a clean kitchen towel to squeeze out excess moisture before adding to the casserole.
✔ Layer ingredients strategically – Start with a thin layer of spaghetti squash, then add filling and cheese to create a firm structure.
4. Why Did My Spaghetti Squash Get Mushy?
If your spaghetti squash turns out too soft or mushy, it’s likely overcooked. Here’s how to fix it:
✔ Roast at 400°F (200°C) for 35-40 minutes – This method keeps it firm and noodle-like.
✔ Check for doneness early – If your squash is small, start checking at 30 minutes.
✔ Let it cool before shredding – Over-shredding hot spaghetti squash releases more liquid.
Final thouth on Spaghetti Squash Enchilada Casserole
Spaghetti Squash Enchilada Casserole is the perfect way to enjoy bold enchilada flavors while keeping your meal healthy, low-carb, and nutrient-rich. By swapping traditional tortillas for spaghetti squash, this casserole becomes a gluten-free, fiber-packed, and anti-inflammatory alternative to a classic comfort food.
We’ve covered everything you need to know to make this casserole perfectly textured, full of flavor, and never watery. From properly roasting and draining the squash to choosing the best toppings and sides, you now have all the tips to customize and enjoy this dish to your preference.
PrintSpaghetti Squash Enchilada Casserole – A Healthy & Flavorful Twist
Spaghetti Squash Enchilada Casserole is a delicious, low-carb twist on classic enchiladas, packed with bold Mexican flavors and wholesome ingredients.
- Prep Time: 15 minutes
- Cook Time: 45 minutes
- Total Time: 1 hour
- Yield: 6 servings
- Category: Dinner
- Method: Baking
- Cuisine: Mexican
- Diet: Gluten Free
Ingredients
- Spaghetti Squash – The star ingredient that gives the casserole a noodle-like texture while keeping it low-carb.
- Shredded Chicken or Black Beans – Choose between shredded chicken for protein or black beans for a vegetarian option.
- Enchilada Sauce – A rich and flavorful sauce that defines the classic enchilada taste. Red, green, or homemade enchilada sauce all work great.
- Bell Peppers & Onions – These vegetables add natural sweetness and texture to your Spaghetti Squash Enchilada Casserole.
- Cheese – A Mexican cheese blend, cheddar, or Monterey Jack gives that classic enchilada casserole texture. Use dairy-free cheese for a vegan-friendly version.
- Spices – Chili powder, cumin, smoked paprika, and garlic powder enhance the flavors.
- Cilantro & Lime – Fresh garnishes that bring out the zesty and bold taste of this casserole.
Instructions
Step 1: Prepare the Spaghetti Squash
Properly cooking spaghetti squash is crucial to avoid a watery Spaghetti Squash Enchilada Casserole. Follow these methods for the best results:
Oven-Roasting (Best for Flavor & Texture)
- Preheat your oven to 400°F (200°C).
- Cut the spaghetti squash in half lengthwise and scoop out the seeds.
- Drizzle with olive oil, sprinkle with salt and pepper, and place the halves cut-side down on a baking sheet.
- Roast for 35-40 minutes until the flesh is tender and easily shredded.
- Let the squash cool slightly, then use a fork to shred it into spaghetti-like strands.
Pro Tip: To remove excess moisture, place the shredded squash in a clean kitchen towel and squeeze out extra liquid before adding it to the casserole.
Microwave Method (Faster, but More Moisture Retention)
- Poke holes in the squash with a fork and microwave for 5-7 minutes to soften.
- Carefully cut in half, scoop out the seeds, and microwave again for another 5 minutes until soft.
- Shred into strands using a fork and drain excess moisture before using.
Step 2: Cook the Enchilada Filling
While the spaghetti squash is cooking, prepare the flavorful enchilada filling:
- Heat 1 tablespoon of olive oil in a large skillet over medium heat.
- Sauté diced onions and bell peppers for about 3-4 minutes until softened.
- Add shredded chicken or black beans, stirring to combine.
- Pour in 1 cup of enchilada sauce and season with chili powder, cumin, and smoked paprika.
- Simmer for 5 minutes, stirring occasionally, until everything is well coated and heated through.
Want more spice? Add chopped jalapeños or a dash of hot sauce!
Step 3: Assemble the Spaghetti Squash Enchilada Casserole
Now it’s time to bring everything together:
- Preheat the oven to 375°F (190°C).
- Layer half of the shredded spaghetti squash at the bottom of a greased baking dish.
- Spread half of the enchilada filling evenly over the squash.
- Sprinkle half of the cheese on top for a gooey, melty texture.
- Repeat the layers with the remaining squash, filling, and cheese.
- Drizzle extra enchilada sauce over the top for added flavor.
Step 4: Bake Until Golden & Bubbly
- Cover the dish with foil and bake for 20 minutes.
- Remove the foil and bake for another 10 minutes until the cheese is melted and slightly golden.
- Let the casserole rest for 5 minutes before serving.
Want extra crisp? Broil the casserole for 2-3 minutes at the end for a golden, bubbly cheese topping.
Step 5: Garnish & Serve
Once your Spaghetti Squash Enchilada Casserole is out of the oven, finish with:
✔ Fresh cilantro
✔ Sliced avocado
✔ A squeeze of lime
✔ Dollop of sour cream or Greek yogurt
Now you’re ready to enjoy a cheesy, comforting, and nutritious enchilada casserole that’s packed with flavor!
Nutrition
- Serving Size: 1 portion (⅙ of casserole)
- Calories: 280 kcal
- Sugar: 6g
- Fat: 14g
- Carbohydrates: 22g
- Fiber: 6g
- Protein: 18g
Keywords: Spaghetti Squash Enchilada Casserole