As I pulled the spaghetti squash from the oven, a wave of savory aroma wrapped around my kitchen like a cozy blanket. These delightful Spaghetti Squash Pizza Nests are more than just a meal; they offer a fun, creative way to enjoy pizza flavors while keeping your carb count low. Each nest features a crispy exterior that cradles a cheesy, satisfyingly soft center, combining the best of pizza and comfort food in one bite. Not only are they gluten-free and keto-friendly, but they also make for quick weeknight dinners or crowd-pleasing appetizers. Have you ever transformed a humble vegetable into a pizza delight? Let’s dive into this delicious adventure together!

Why Are These Pizza Nests Unique?
Delightfully Unique: Transforming spaghetti squash into pizza nests offers a creative twist on a beloved classic.
Low-Carb Wonder: These nests satisfy your pizza cravings without the guilt, ideal for keto lovers or anyone looking to reduce carbs.
Family-Friendly Fun: Kids adore these bite-sized creations, making them perfect for family dinner nights or casual gatherings.
Quick to Prepare: With simple ingredients and easy steps, you’ll have a delicious meal in no time!
Versatile Flavors: Feel free to experiment by swapping toppings or using different sauces, just like with our Muffin Breakfast Pizzas.
Wholesome Ingredients: Packed with nutrients yet loaded with flavor, these nests are a health-conscious choice without compromising on taste.
Spaghetti Squash Pizza Nests Ingredients
For the Nests
• Spaghetti Squash – This serves as the delicious, low-carb base, providing about 2.5 cups of squash noodles once cooked.
• Eggs – Acts as the binder, uniting the squash; a flax egg can substitute with 1 tbsp flax meal and 3 tbsp water for a vegan option.
For the Sauce Mixture
• Tomato Sauce – Adds moisture and flavor; opt for a brand without added sugars for healthier benefits.
• Garlic Powder – Enhances taste profiles; fresh garlic can bring an even bolder flavor if preferred.
• Italian Seasonings – Infuses savory Italian flair; fresh herbs can elevate the flavor profile.
• Oregano – Contributes a distinctive Mediterranean taste; additional Italian seasoning can serve as a substitute if needed.
• Sea Salt – Elevates all flavors; adjust based on your taste preferences.
For the Toppings
• Pepperoni – Infuses classic pizza flavor and protein; choose uncured, nitrate-free options for a healthier touch.
• Mozzarella Cheese – Offers creaminess and richness; use dairy-free cheese for a vegan twist.
• Basil – Adds freshness; dried basil works well in a pinch.
Step‑by‑Step Instructions for Spaghetti Squash Pizza Nests
Step 1: Preheat the Oven
Begin by preheating your oven to 400°F (204°C). While the oven heats up, prepare a baking sheet by lightly greasing it with oil or lining it with parchment paper. This will provide a non-stick surface for the spaghetti squash and allow for easy cleanup once your delicious Spaghetti Squash Pizza Nests are ready.
Step 2: Bake the Spaghetti Squash
Use a sharp knife or skewer to poke several holes in the spaghetti squash, allowing steam to escape while it bakes. Place it on the prepared baking sheet and bake for about 60 minutes, turning halfway through to ensure even cooking. Once done, it should be tender enough to easily pierce with a fork.
Step 3: Cool and Scrape the Squash
After baking, let the spaghetti squash cool for at least 15 minutes. Once it’s cool enough to handle, cut it in half lengthwise and use a fork to scrape the flesh into a bowl, creating the spaghetti-like strands. This tender squash will serve as the base for your flavorful Pizza Nests.
Step 4: Prepare the Muffin Pans
Grease two muffin pans with oil to prevent sticking. Then, in a separate bowl, combine the tomato sauce, garlic powder, Italian seasonings, and oregano. Mix well to ensure an even distribution of flavors that will beautifully complement the pizza nests.
Step 5: Mix the Noodle Batter
Incorporate the beaten eggs into the bowl with the scraped spaghetti squash, mixing thoroughly to bind the noodles together. This egg mixture will be the base for your Spaghetti Squash Pizza Nests. Carefully fill each greased muffin cup with the noodle mixture, aiming to form a well in the center for the sauce.
Step 6: Add Sauce and Toppings
Spoon the prepared tomato sauce mixture evenly into each well you created in the muffin cups. Top each nest with a slice of pepperoni for that classic pizza flavor. Finally, add a sprinkle of mozzarella cheese and a touch of fresh basil on top to enhance the flavor profile of your delightful nests.
Step 7: Bake the Nests
Place the filled muffin tins back in the oven and bake for an additional 25 minutes at 400°F (204°C). Keep an eye on them, as the nests should be set and gently golden on top. They’ll emerge from the oven smelling delicious and ready to be enjoyed as satisfying, low-carb bites!

Spaghetti Squash Pizza Nests Variations
Feel free to play with your recipe and add unique touches that excite your taste buds!
- Dairy-Free: Substitute mozzarella with your favorite dairy-free cheese to enjoy a vegan version that’s just as scrumptious.
- Vegetarian Delight: Leave out the pepperoni and opt for roasted veggies like zucchini, bell peppers, or mushrooms for a hearty, plant-based option.
- Spicy Kick: Add crushed red pepper flakes or jalapeños to the sauce for a delightful heat that spices things up.
- Zucchini Noodles: For an extra veggie boost, replace half the spaghetti squash with zucchini noodles for a refreshing texture.
- Herb-Infused: Swap the oregano for fresh thyme or herbes de Provence to give your nests a new flavor profile; the fresh herbs elevate the dish!
- BBQ Twist: Exchange tomato sauce for BBQ sauce for a sweet and smoky version of these nests, perfect for summer vibes.
- Protein Boost: Mix in some cooked ground turkey or chicken with your sauce; it’s a fantastic way to pack in extra protein.
- Mediterranean Style: Add Kalamata olives and feta cheese for a Mediterranean flair that will invigorate your palate and transport you straight to Greece.
Want to explore more delicious ideas? Check out these Muffin Breakfast Pizzas or our vibrant Asparagus Zucchini Squash for even more culinary inspiration!
Expert Tips for Spaghetti Squash Pizza Nests
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Pre-Bake Tip: Microwave your spaghetti squash for 3-5 minutes before baking to soften it, making it easier to cut and scrape later.
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Moisture Management: Avoid excess water in your nests by thoroughly scraping the squash and letting it drain in a colander for a few minutes before mixing.
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Watch the Timer: Keep an eye on baking time—remove the nests once they are golden and firm. Overbaking can lead to dryness, so stay vigilant!
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Flavor Infusion: Enhance the taste of your Spaghetti Squash Pizza Nests by adding extra seasonings or fresh herbs to the tomato sauce for a burst of flavor.
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Topping Flexibility: Experiment with toppings! Swap out the pepperoni for turkey bacon or add sautéed vegetables to cater to your personal preferences.
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Serving Size: These nests make a great appetizer or light meal. Consider doubling the recipe for gatherings, ensuring everyone gets to enjoy these delicious, low-carb bites!
Make Ahead Options
These Spaghetti Squash Pizza Nests are a fantastic choice for meal prep! You can bake the spaghetti squash and scrape it into strands up to 24 hours in advance, storing it in an airtight container in the refrigerator to keep it fresh. Additionally, you can pre-mix the tomato sauce and seasonings, allowing all the flavors to meld effectively. When you’re ready to serve, simply combine the squash and eggs, fill the muffin cups, add the sauce, pepperoni, and cheese, and bake! This prep approach saves you valuable time during busy weeknights while ensuring each nest retains its delicious texture and flavor. Enjoy homemade goodness without the rush!
How to Store and Freeze Spaghetti Squash Pizza Nests
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Room Temperature: It’s best to avoid leaving cooked Spaghetti Squash Pizza Nests at room temperature for more than 2 hours to prevent bacterial growth.
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Fridge: Store leftovers in an airtight container in the refrigerator for up to 5 days. Simply reheat in the microwave or oven for a warm, quick snack.
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Freezer: For longer storage, freeze the nests in an airtight container or freezer bag for up to 2 months. Thaw in the fridge overnight before reheating.
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Reheating: To reheat, place in a preheated oven at 350°F (175°C) for about 15 minutes, or microwave on medium heat until warmed through, ensuring the crispy texture remains!
What to Serve with Spaghetti Squash Pizza Nests
These delightful bites deserve a delightful spread to elevate your meal experience even further.
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Crunchy Salad: A fresh garden salad adds a vibrant balance, with crisp veggies and zesty dressing complementing the cheesy nests.
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Garlic Breadsticks: These buttery, garlicky treats bring warmth and comfort, perfect for dipping into leftover sauce from your pizza nests.
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Roasted Vegetables: Seasonal roasted veggies like zucchini and bell peppers provide a sweet contrast to the savory nests, adding depth to your plate.
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Balsamic Glazed Brussels Sprouts: The tangy-sweet glaze perfectly enhances the flavor of both the sprouts and the pizza nests, making for a pairing to remember.
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Classic Caesar Salad: Creamy dressing, crunchy croutons, and fresh romaine lettuce amplify the meal’s richness while keeping it light.
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Sparkling Water with Lemon: A refreshing drink like sparkling water enhances flavors and refreshes the palate after each cheesy bite, making for an uplifting dining experience.

Spaghetti Squash Pizza Nests Recipe FAQs
What is the best way to select a spaghetti squash?
Absolutely! When choosing a spaghetti squash, look for a firm, yellow or golden rind without soft spots or dark blemishes. A squash that feels heavy for its size is often a sign of ripeness, usually weighing around 3-5 pounds.
How should I store leftover spaghetti squash pizza nests?
Very! Store your Spaghetti Squash Pizza Nests in an airtight container in the refrigerator for up to 5 days. Just make sure they’re cooled down to room temperature before sealing. Reheat them in the microwave or oven when you’re ready to enjoy them again.
Can I freeze spaghetti squash pizza nests, and if so, how?
Of course! To freeze your nests, first allow them to cool completely. Place them in a single layer on a baking sheet to freeze for several hours. Once frozen, transfer them to a freezer bag or an airtight container. They can be stored for up to 3 months. When ready to eat, thaw in the fridge overnight and reheat as mentioned above.
What should I do if my spaghetti squash nests are too soggy?
I get it! If your nests come out a bit soggy, that might be due to excess moisture from the squash. To troubleshoot, make sure to thoroughly scrape out the squash and let it drain in a colander for a few minutes before mixing. You can also bake them a little longer to help them firm up, keeping an eye on them to avoid over-baking.
Are these pizza nests suitable for people with allergies?
Absolutely! Our Spaghetti Squash Pizza Nests can be allergen-friendly. If you’re cooking for someone with egg allergies, you can replace eggs with flax eggs (1 tbsp of flax meal + 3 tbsp of water). Also, if dairy is a concern, using a dairy-free cheese alternative works perfectly! Just be cautious about the specific toppings you choose to ensure they’re safe for any guests with dietary restrictions.
How do I know when my spaghetti squash is perfectly cooked?
Very! Your spaghetti squash should be lightly golden and easily pierced with a fork when properly cooked. The strands should be tender but not mushy—this way, they’ll hold their structure well when baking into nests. If you poke it and it feels hard, give it a bit more time in the oven!

Delicious Spaghetti Squash Pizza Nests for Low-Carb Cravings
Ingredients
Equipment
Method
- Preheat your oven to 400°F (204°C) and prepare a baking sheet by lightly greasing it.
- Poke several holes in the spaghetti squash and bake for about 60 minutes, turning halfway.
- Let the spaghetti squash cool for at least 15 minutes, then cut it in half and scrape the flesh into a bowl.
- Grease the muffin pans and combine the tomato sauce, garlic powder, Italian seasonings, and oregano in a separate bowl.
- Mix the beaten eggs into the bowl with the scraped spaghetti squash and fill each greased muffin cup.
- Spoon the tomato sauce mixture into each well and top with pepperoni, mozzarella cheese, and basil.
- Bake filled muffin tins at 400°F (204°C) for an additional 25 minutes until golden.

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