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Home » Pizza Recipes » Spaghetti Squash Pizza

Spaghetti Squash Pizza

A photo of Vered DeLeeuw.
by Vered DeLeeuwUpdated Jun 30, 2025
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5 from 2 votes

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This delicious spaghetti squash pizza is ready in less than an hour. It combines the flavors and cheesiness of pizza with a better-for-you vegetable base.

Spaghetti squash pizza is served on a white plate.

When my kids ask if we can order pizza and I have spaghetti squash in the house, I ask them if they would like this veggie-based pizza instead. Nine times out of ten, the enthusiastic answer is "Yes!" So this should tell you how good it is. It's genius, really - enjoy all the cheesiness and goodness of pizza but with a vegetable base.

Ingredients

The ingredients needed to make spaghetti squash boats.

See the recipe card for exact measurements. Here are my comments on some of the ingredients.

  • Spaghetti squash: I use a small, 2-pound squash.
  • Marinara sauce: I use a sugar-free sauce such as Rao's.
  • Cheese: I use shredded part-skim mozzarella.
  • Topping: I use pepperoni.
  • Grated parmesan: It's best to use finely grated parmesan and not coarsely shredded, although if all you have is shredded, you can use that.

Variations

  1. You can use different melty cheeses instead of mozzarella. Provolone is a good option.
  2. You can use whatever toppings you like and enjoy. I like to use pepperoni, but other options include olives, sautéed mushrooms, red onions, and bell peppers.
  3. Sometimes, I mix a cup of shredded baked chicken breast into the squash.

Instructions

The detailed instructions and step-by-step photos are included in the recipe card. Here's a quick overview.

Cook the squash. You can microwave the squash or bake it. Rake a fork back and forth to remove strands of the flesh, keeping the shells intact.

Spaghetti squash strands in a glass bowl.

Mix the strands with marinara sauce and shredded mozzarella, then transfer them back to the shells. Arrange the pepperoni on top and sprinkle the squash halves with the remaining mozzarella and parmesan.

The boats are ready for the oven.

Bake until the cheese is melted and lightly browned, about 15 minutes. Let rest for five minutes before serving.

The boats are ready in the pan.

Recipe Tip

When you rake the squash's flesh to create the strands, work carefully so that the shells remain intact, and leave some flesh in the shells.

But if the shells get torn despite all your best efforts, do not despair. Simply bake the filling in a casserole dish like a square 8-inch baking dish. It won't be as pretty, but it will be just as delicious!

Recipe FAQs

Is it better to microwave or bake the squash?

I like to microwave it because it's faster, but baking does yield superior results in terms of texture and flavor. Microwaved squash can be a little mushy.

Can I eat the squash's skin?

Theoretically, you could, but I don't think it would be a very pleasant experience. Once baked in the oven, the skin will be tough and dry.

Why do you pierce the squash before microwaving it?

Piercing helps prevent it from exploding in the microwave.

How long can I keep the leftovers?

You can keep the leftovers in an airtight container in the fridge for 3-4 days. They keep well! Reheat them covered in the microwave at 50% power or uncovered in a 350°F oven. I don't recommend freezing the leftovers.

Serving Suggestions

I usually serve spaghetti squash pizza as a main course, alongside a simple green vegetable that I can cook in the same 425°F oven, like roasted Brussels sprouts, roasted green beans, or roasted broccolini.

You can also serve it with an easy side salad like arugula salad, cucumber vinegar salad, or cherry tomato salad.

When I serve it as a side dish, I pair this pizza with a main course I can cook in the same oven, like chicken leg quarters, baked salmon, and roasted rack of lamb.

Recipe Card

Spaghetti squash pizza is served on a white plate.
5 from 2 votes
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Spaghetti Squash Pizza Recipe

This delicious spaghetti squash pizza is ready in less than an hour. It combines the flavors and cheesiness of pizza with a better-for-you vegetable base.
Prep Time30 minutes mins
Cook Time15 minutes mins
Rest time5 minutes mins
Total Time50 minutes mins
Course: Side Dish
Cuisine: American
Servings: 2 servings
Calories: 270kcal
Author: Vered DeLeeuw
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Ingredients

  • 2 pounds spaghetti squash
  • ½ cup marinara sauce
  • 4 ounces part-skim mozzarella - shredded, divided
  • Dash sea salt
  • Dash black pepper
  • 1 ounce pepperoni
  • 2 tablespoons parmesan - grated
  • 2 tablespoons parsley - chopped

Instructions

  • Preheat the oven to 425°F.
    An oven set to 425°F.
  • Cook the spaghetti squash in the microwave: wipe the skin clean, pierce it in a few places with a sharp knife, place it on a microwave-safe plate, and microwave on high until tender, for about 5 minutes on each side.
    Microwaving the squash.
  • Allow the cooked squash to rest for 10 minutes until cool enough to handle. Cut it open with a sharp knife. Use a large spoon to discard the pulp and seeds. Rake a fork back and forth to create spaghetti-like strands, placing the strands in a large mixing bowl. Work carefully so that the shells remain intact, and leave some flesh in the shells.
    Spaghetti squash strands in a glass bowl.
  • Add the marinara sauce to the spaghetti squash strands. Mix well to coat. Mix in 2 ounces of the shredded mozzarella.
    Adding marinara sauce to the squash.
  • Sprinkle the inside of the squash shells with salt and pepper. Transfer the marinara-coated strands back into the shells. Arrange the pepperoni on top and sprinkle the squash with the remaining mozzarella and with parmesan.
    The boats are ready for the oven.
  • Place the squash shells in a square 8-inch baking dish, or any other baking dish that will hold them snugly. Bake until the cheese is melted and lightly browned, about 15 minutes.
    The boats are ready in the pan.
  • Remove the pan from the oven. Sprinkle the pizza with parsley. Allow it to cool for about 5 minutes, then serve.
    Spaghetti squash boats are served.

Notes

  • When you rake the squash's flesh to create strands, work carefully so that the shells remain intact, and leave some flesh in the shells. But if, despite your best efforts, the shells get torn, do not despair. Simply bake the filling in a casserole dish, such as a square 8-inch baking dish. It won't be as pretty, but it will be just as delicious!
  • You can use whatever toppings you like and enjoy. I like to use pepperoni, but other options include olives, sautéed mushrooms, red onions, and bell peppers.
  • You can mix a cup of shredded baked chicken breast into the squash.
  • You can keep the leftovers in an airtight container in the fridge for 3-4 days. They keep well! Reheat them covered in the microwave at 50% power or uncovered in a 350°F oven. I don't recommend freezing the leftovers.

Nutrition per Serving

Serving: 0.5 recipe | Calories: 270 kcal | Carbohydrates: 14 g | Protein: 20 g | Fat: 15 g | Saturated Fat: 7 g | Sodium: 816 mg | Fiber: 3 g | Sugar: 6 g

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Most recipes are low-carb and gluten-free, but some are not. Recommended and linked products are not guaranteed to be gluten-free. Nutrition info is approximate. Please verify it independently. The carb count excludes non-nutritive sweeteners. Please read these Terms of Use before using any of my recipes.

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Healthy Recipes Blog was founded in 2011 by Vered DeLeeuw. It features real food recipes with a focus on low-carb and gluten-free ingredients. All recipes are nutritionally reviewed by a Registered Dietitian. Contact us at HealthyRecipesBlog@gmail.com.

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