A Pizza Lover’s Healthy Awakening
Friday night pizza traditions were sacred in our household until my teenage daughter announced she was going gluten-free for health reasons. Suddenly, our beloved family pizza nights seemed impossible. After weeks of disappointing gluten-free crusts and expensive alternatives, I stumbled upon spaghetti squash at the farmer’s market. The vendor mentioned using it as a pasta substitute, but something sparked in my mind – why not pizza? That evening, I created these Pepperoni Pizza Spaghetti Squash Boats, and our family tradition was beautifully restored. Now, even my husband (the biggest pizza purist I know) requests these boats over traditional pizza!
Why This Recipe Will Transform Your Pizza Nights
All the Pizza Flavor, None of the Guilt
These squash boats deliver every element you crave in pizza: tangy marinara sauce, melted mozzarella, savory pepperoni, and aromatic herbs. However, they provide significantly fewer calories and carbs while adding a full serving of vegetables to your meal.
Naturally Portion-Controlled
Unlike traditional pizza where it’s easy to eat slice after slice, these boats naturally limit portions while still feeling incredibly satisfying. Each half provides the perfect amount of food without leaving you uncomfortably full.
Impressive Presentation with Minimal Effort
Serving dinner in the squash shells creates an Instagram-worthy presentation that makes weeknight meals feel special. Furthermore, cleanup is surprisingly simple since you’re essentially eating the serving dish!
Diet-Friendly for Everyone
Whether you’re following keto, low-carb, gluten-free, or simply trying to eat more vegetables, this recipe accommodates virtually every dietary preference without compromising on taste.
Essential Ingredients
For the Squash Base
- 1 medium spaghetti squash (about 3 pounds)
- 2 teaspoons olive oil
- 1/4 teaspoon kosher salt
- 1/4 teaspoon freshly ground black pepper
For the Pizza-Style Sauce
- 1/2 cup marinara sauce (low-sugar preferred)
- 1/2 teaspoon dried oregano
- 1/2 teaspoon dried basil
- 1/4 teaspoon crushed red pepper flakes (optional)
For the Toppings
- 1/2 cup shredded mozzarella cheese
- 1/4 cup sliced turkey pepperoni
- 1 tablespoon grated Parmesan cheese
- Fresh chopped parsley for garnish (optional)
Serving Suggestions
This recipe serves 2 as a hearty main course or 4 as a substantial side dish. Pair with a crisp green salad dressed with balsamic vinaigrette, or serve alongside roasted Brussels sprouts for a complete, nutritious meal.
Step-by-Step Instructions
Preparing the Squash Foundation
- Set up for roasting: Preheat your oven to 400°F (200°C) and line a large baking sheet with parchment paper. This prevents sticking and makes cleanup effortless.
- Prepare the squash: Cut the spaghetti squash in half lengthwise using a sharp knife. Remove all seeds and stringy pulp from the center cavity using a spoon or ice cream scoop.
- Season and oil: Brush the inside of each squash half with olive oil, ensuring even coverage. Sprinkle with kosher salt and freshly ground black pepper.
- Initial roasting: Place the squash halves cut-side down on the prepared baking sheet. Roast for 35-40 minutes, until the flesh yields easily to a fork.
Creating the Pizza Elements
- Prepare the squash strands: Remove the squash from the oven and carefully flip each half over. Allow to cool for 5 minutes, then use a fork to gently loosen the flesh into spaghetti-like strands, keeping them nestled in their shells.
- Make the pizza sauce: While the squash cools, combine the marinara sauce with oregano, basil, and red pepper flakes (if using) in a small bowl. This herb-infused sauce mimics classic pizza flavors perfectly.
Assembly and Final Cooking
- Add the sauce: Divide the seasoned marinara sauce evenly between the two squash halves. Gently stir to coat the squash strands without breaking them.
- Layer the cheese: Sprinkle the mozzarella cheese generously over each boat, ensuring even distribution for optimal melting.
- Top with pepperoni: Arrange the turkey pepperoni slices across the surface, then finish with a sprinkle of Parmesan cheese for extra flavor depth.
- Final bake: Return the boats to the oven for 10-12 minutes, until the cheese is bubbly and lightly golden around the edges.
- Garnish and serve: Remove from oven and garnish with fresh chopped parsley if desired. Serve immediately while the cheese is still gloriously melted.

Creative Serving Ideas
Family-Style Presentation
Place both boats on a large wooden cutting board with small forks for easy sharing. Add some cherry tomatoes and fresh basil leaves around the boats for an Italian-inspired presentation.
Individual Portions
For dinner parties, scrape the finished mixture from the shells and serve in individual ramekins topped with extra cheese and briefly broiled for a bubbling finish.
Delicious Recipe Variations
Supreme Pizza Version
Add diced bell peppers, sliced mushrooms, and red onions to the marinara sauce before assembling. Use a combination of mozzarella and cheddar cheese for extra richness.
Meat Lovers’ Style
Include crumbled turkey sausage along with the pepperoni, and add a sprinkle of crispy bacon bits just before serving. This variation satisfies the heartiest appetites.
Veggie Delight
Replace the pepperoni with roasted vegetables like zucchini, bell peppers, and cherry tomatoes. Add fresh basil and a drizzle of pesto after baking for Mediterranean flair.
White Pizza Inspired
Skip the marinara and instead brush the squash with garlic-infused olive oil. Top with ricotta cheese, mozzarella, and fresh herbs for a sophisticated twist.
Make-Ahead and Storage Tips
Advance Preparation
The spaghetti squash can be roasted and prepared up to 2 days ahead of time. Store the scraped squash in the shells, covered tightly with plastic wrap in the refrigerator until ready to assemble.
Meal Prep Strategy
Prepare multiple boats on Sunday and store them assembled but unbaked in the refrigerator. During the week, simply pop them in the oven for a quick, healthy dinner.
Freezing Instructions
These boats freeze beautifully for up to 2 months. Assemble completely but don’t bake, then wrap tightly in plastic wrap and aluminum foil. Thaw overnight in the refrigerator before baking as directed.
Important Notes
Squash Selection Tips
Choose spaghetti squash that feels heavy for its size with hard, unblemished skin. The color should be pale yellow rather than green, indicating full ripeness. Avoid squash with soft spots or dark patches.
Pepperoni Considerations
Turkey pepperoni provides excellent flavor with less fat than traditional pork varieties. However, you can substitute with any sliced pepperoni you prefer, or even use plant-based alternatives for vegetarian versions.
Texture Perfection
Don’t over-scrape the squash flesh, as this can result in mushy strands. The goal is to maintain some texture that resembles al dente pasta for the best eating experience.

Frequently Asked Questions
How do I prevent the squash boats from being watery? After scraping the squash strands, let them sit for 5-10 minutes and gently pat with paper towels to remove excess moisture. This prevents the final dish from becoming soggy and ensures better cheese melting.
Can I use regular pepperoni instead of turkey pepperoni? Absolutely! Traditional pepperoni works perfectly in this recipe. Turkey pepperoni simply offers a leaner option with similar flavor. Choose whichever fits your dietary preferences.
What if I don’t like spicy food? Simply omit the red pepper flakes from the sauce mixture. The oregano and basil will still provide plenty of pizza-inspired flavor without any heat.
How can I make this recipe dairy-free? Use your favorite dairy-free mozzarella cheese alternative, or skip the cheese entirely and add extra vegetables and herbs. Nutritional yeast also provides a pleasant cheesy flavor for dairy-free diets.
Can I add other pizza toppings? Definitely! This recipe serves as an excellent base for any pizza toppings you enjoy. Just remember that vegetables with high water content should be pre-cooked to prevent excess moisture.
Is this recipe suitable for meal prep? Yes! These boats reheat beautifully in the oven at 350°F for 15-20 minutes. They also work well for lunch the next day, either reheated or enjoyed cold as a unique salad.
How do I know when the spaghetti squash is properly cooked? The squash is ready when you can easily pierce the skin with a fork and the flesh gives slightly to pressure. Under-cooked squash will be difficult to scrape into strands, while over-cooked squash becomes mushy.
Can I make smaller portions? Yes! Use two smaller spaghetti squash instead of one large one, or scrape the cooked squash completely from the shells and serve individual portions in small baking dishes.
Prep Time: 10 minutes | Cooking Time: 50 minutes | Total Time: 60 minutes
Calories: 320 kcal | Servings: 2 servings