Spaghetti Squash Pizza Casserole Recipe with Melty Cheese

The familiar comfort of cheesy pepperoni pizza, reimagined over roasted spaghetti squash with sautéed mushrooms, onions and seasoned ground chicken tossed in pizza sauce. This spaghetti squash pizza casserole is a flavorful, lower-carb twist on traditional pizza that’s perfect for weeknight dinners, meal prep, or a potluck. Below I’ll walk you through how to make it step by step.

This is a picture of a baking dish with cooked spaghetti squash pizza casseole.

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Why This Recipe Works

  • All the pizza flavor with fewer carbs and fewer calories. Roasted spaghetti squash replaces traditional crust while retaining the satisfying combo of pizza sauce, melted cheese and pepperoni. Ground chicken, mushrooms, and onions add texture and protein. The dish is naturally gluten free.
  • Easy to customize. Swap ground chicken for ground beef, Italian sausage, a vegetarian ground substitute, or omit meat altogether. Add your favorite pizza vegetables — bell peppers, spinach, artichokes — and use whatever pepperoni you prefer.
  • Family friendly and practical. This casserole is comforting, nutritious, reheats well, and works great for meal prep or feeding a crowd.
This is a close up picture of the spaghetti squash pizza casserole.

Key Ingredients

  • Spaghetti squash — a mild, slightly firm squash that’s low in carbs and calories and provides fiber and nutrients.
  • Ground meat — ground chicken keeps the dish lean; substitute any ground meat you like.
  • Pizza sauce — I prefer pizza sauce for a more authentic pizza flavor, but marinara works fine too.
  • Pepperoni — use your favorite style and size.
  • Shredded cheese — mozzarella or an Italian blend melts best; shredding from a block yields the best melt and texture.
This is a picture of all the ingredients to make the spaghetti squash pizza casserole.

How To Cut and Roast A Spaghetti Squash

This is a picture of the squash with the ends cut off.

Begin by trimming both ends of the squash so it sits flat on the cutting board.

This is a picture of the squash cut in half.

Carefully slice the squash in half lengthwise with a sharp knife. Some larger or firmer squash require more effort—take care and go slowly.

This is a picture of the seeds being removed from the inside of the squash.

Scrape out the seeds and strings with a sturdy spoon. You can discard them or roast the seeds like pumpkin seeds.

This is a picture of the two halves of the squash with oil, salt and pepper.

Place the halves on a parchment-lined baking sheet, spray or brush with oil, and season with salt and pepper.

This is a picture of the two halves of the squash flesh down on the baking sheet.

Turn the halves flesh-side down, poke a few holes with a fork, and roast at 400°F (200°C) for 35–45 minutes, or until tender when pierced.

This is a picture of the squash being scrapped with a fork to make the spaghetti strings.

Allow the squash to cool until it’s safe to handle, then use a fork to scrape the flesh into spaghetti-like strands. Discard the skins and set the strands aside.

How To Make This Recipe

  • Roast the spaghetti squash first, then prepare the filling and assemble the casserole.
This is a picture of a skillet with onion cooking.

Heat the oil in a large skillet over medium-high heat and cook the diced onion until translucent, about 5 minutes.

This is a picture of a skillet with onion and mushrooms cooking.

Add sliced mushrooms and cook another 3–4 minutes until they soften.

This is a picture of the skillet with the added chicken.

Push the vegetables to one side, add a splash of oil if needed, and brown the ground chicken with Italian seasoning, salt and pepper. Cook until no longer pink, then combine with the vegetables.

This is a picture of the skillet with the added garlic.

Drain excess liquid from the pan, create a small well, add the minced garlic and cook briefly until fragrant, about 1 minute.

This is a picture of the skillet with the added pizza sauce.

Stir in the pizza sauce, bring to a gentle simmer and cook a few minutes to combine flavors.

This is a picture of the skillet with the added squash.

Fold in the shredded spaghetti squash until everything is evenly combined.

This is a picture of the baking dish with the chicken and squash mixture.

Transfer the mixture to a lightly oiled baking dish in an even layer.

This is a picture of the baking dish with the chicken and squash mixture topped with cheese.

Top evenly with shredded cheese.

This is a picture of the baking dish with the chicken and squash mixture, cheese and pepperoni on top.

Arrange pepperoni over the cheese and bake in a preheated 375°F (190°C) oven for 20–25 minutes, until the top is golden and bubbly. Optionally broil briefly (1–3 minutes) for extra browning.

This is a picture of the baking dish with the spaghetti squash pizza casserole out of the oven.

Remove from the oven, let the casserole rest 5–10 minutes, garnish with fresh basil, and serve warm. Enjoy!

This is a picture of the dish in the baking dish ready to eat.

Frequently Asked Questions

My casserole is a little soupy — how can I fix it?

  • Spaghetti squash can hold water. To reduce excess moisture, place the cooked shredded squash in a colander and press gently with a spoon to drain some liquid before mixing with the sauce.

What should I serve with it?

  • This casserole pairs well with a crisp side salad or a piece of crusty bread if you want extra carbs.

Tips

  • Watch the squash closely. Smaller squash cook faster; 35–40 minutes is typical but ovens vary.
  • Let it rest. Allow the baked casserole to sit 5–10 minutes to firm up before serving.
  • Make it spicy. Add red pepper flakes, spicy sausage, or hot pepperoni to increase heat.
  • Storage. Store leftovers in an airtight container in the refrigerator for up to 4 days.
This is a close up picture of the casserole.

Recipe Summary

Square picture of the spaghetti squash pizza casserole.

Spaghetti Squash Pizza Casserole

The comfort of cheesy pepperoni pizza on roasted spaghetti squash with sautéed mushrooms, onions and seasoned ground chicken tossed in pizza sauce.
Prep Time 15 mins
Cook Time 1 hr 15 mins
Total Time 1 hr 30 mins
Course Main Course
Cuisine American
Servings 6 servings
Calories 276.9 kcal

Ingredients

  • 1 spaghetti squash
  • spray cooking oil
  • salt and black pepper, to taste
  • 1 tablespoon olive or avocado oil
  • ½ yellow onion, diced
  • 3 cloves garlic, minced
  • 8–10 sliced mushrooms (about 1½ cups)
  • 1 pound ground chicken (or preferred ground meat)
  • 1 teaspoon Italian seasoning
  • 1¼ cups pizza sauce (or marinara)
  • 1 cup shredded Italian four-cheese blend or mozzarella
  • 8–10 pepperoni slices
  • Fresh basil, chopped or chiffonade, for garnish

Instructions

Prepare and Roast the Spaghetti Squash

  • Preheat oven to 400°F (200°C). Line a baking sheet with parchment paper.
  • Trim the ends of the squash and carefully slice it in half lengthwise.
  • Use a sturdy spoon to remove seeds and strings.
  • Place halves flesh-side up, spray with cooking oil, season with salt and pepper, then turn flesh-side down and poke a few holes with a fork.
  • Roast 35–45 minutes, until tender when pierced. Let cool, then scrape the flesh into strands and discard skins.

Make the Casserole

  • Reduce the oven to 375°F (190°C).
  • Heat oil in a large skillet over medium-high. Add diced onion and cook until translucent, about 5 minutes.
  • Add mushrooms and cook 3–4 minutes more.
  • Push vegetables to the side, add a little more oil, and brown the ground chicken with Italian seasoning, salt and pepper. Mix with the vegetables and cook a few minutes until cooked through.
  • Drain excess liquid, add garlic to the pan and cook 1 minute.
  • Stir in pizza sauce and simmer 3–4 minutes.
  • Add the shredded spaghetti squash and combine evenly.
  • Transfer the mixture to a lightly oiled baking dish in a single layer. Sprinkle with shredded cheese and arrange pepperoni on top.
  • Bake 20–25 minutes until cheese is bubbly and golden. Let rest 5–10 minutes, garnish with basil, and serve.

Notes

  • Pepperoni: Use as many or as few slices as you like; larger slices will cover more surface.
  • Stubborn squash: If the squash is very firm, poke holes in the skin and microwave it 2–4 minutes to soften slightly before cutting.
  • The nutrition values are approximate and will vary with ingredient brands and portion sizes.

Nutrition

Serving: 1 serving |
Calories: 276.9 kcal |
Carbohydrates: 17 g |
Protein: 21.1 g |
Fat: 13.6 g
Picture of Priscilla Lawrence owner of Sprinkled with Balance.

About Priscilla Lawrence

Hi, I’m Priscilla Lawrence. Welcome to Sprinkled With Balance, where I share approachable, nutrient-rich recipes that are simple and satisfying. I’m a recipe developer, former certified nutritionist, and food photographer based in California.