Ultimate Cheesy Low-Carb Spaghetti Squash Boats: A Delicious Keto and Gluten-Free Meal
Discover the ultimate low-carb comfort food with these incredible Cheesy Spaghetti Squash Boats! Baked to perfection directly in their own shells, these flavorful boats offer a truly satisfying and wholesome meal. Not only are they naturally gluten-free and keto-friendly, but they’re also packed with festive flavor, making them perfect for any occasion. This recipe is designed to yield generous portions, ensuring you have delicious leftovers that are incredibly easy to reheat, providing a delightful meal for the next day without any extra fuss.

My journey with spaghetti squash started with a humorous mishap. The very first time I ventured to cook spaghetti squash at home, I found myself in a bit of a culinary predicament. Unbeknownst to me, I had mistakenly purchased a butternut squash! At that point, my experience with winter squashes was non-existent, and I couldn’t tell one from the other. My partner, Jason, certainly got a good laugh out of my rookie mistake, but it became a memorable starting point for my love affair with spaghetti squash.
Since that initial, comical attempt, I’ve become quite adept at preparing spaghetti squash, transforming it into a staple in our kitchen. It has quickly become one of our absolute favorite ways to enjoy a “pasta night” experience without the heavy, starchy carbohydrates typically found in traditional pasta. For those seeking a healthier alternative or following a low-carb, keto, or gluten-free diet, spaghetti squash is an absolute game-changer.
The beauty of spaghetti squash lies in its incredible versatility. It truly is a blank canvas, ready to soak up any flavors you throw its way. We’ve explored countless variations for dinner: from light and zesty pesto with fresh parmesan, to hearty chicken and melted cheese, or even a fun, pizza-inspired version with mozzarella and pepperoni. The possibilities are virtually endless, and you could spend days searching for the most elaborate spaghetti squash recipes. However, sometimes, simplicity reigns supreme, and a classic, comforting meal is exactly what you need. That’s why I absolutely adore baking my low-carb spaghetti squash with a rich ricotta cheese mixture, then generously layering it with vibrant marinara sauce and fresh mozzarella, creating an experience that’s both familiar and wonderfully fresh.

When it comes to marinara sauce, I have a firm philosophy: if I have the time and ingredients, I will absolutely make my own. There’s something incredibly satisfying about a homemade sauce, and I often freeze large batches to have on hand for quick and easy meal prep throughout the week. However, life often gets busy, unexpected events crop up, and sometimes you simply don’t have an extra batch in the freezer or the precious time needed to whip up a sauce from scratch. In these moments, there’s absolutely no shame in reaching for a high-quality store-bought jarred sauce. For this particular recipe, a good quality jarred marinara works perfectly and ensures that these cheesy spaghetti squash boats remain a fantastic, stress-free option for an easy weeknight dinner. Look for brands with minimal added sugars and wholesome ingredients to keep it aligned with a low-carb lifestyle.

Essential Tips for Cooking Spaghetti Squash Perfectly
This recipe for Low Carb Spaghetti Squash Parmesan Boats specifically calls for baking your spaghetti squash in the oven, as this method allows the squash to cook gently while retaining its natural “boat” shape – perfect for filling and serving! Baking also brings out a lovely sweetness and ensures the strands are tender yet firm enough to mimic pasta.
However, if oven baking isn’t convenient or you’re looking to speed things up, there are alternative methods to cook your spaghetti squash:
- **Microwave Method (for a quick casserole):** If you prefer to turn this into a delightful spaghetti squash casserole rather than individual boats, the microwave is a fantastic time-saver. Simply poke the squash all over with a fork (to allow steam to escape), then microwave it whole for approximately 15 minutes, or until it feels tender when squeezed (be careful, it will be hot!). Remove it from the microwave using a towel or oven mitts, allow it to cool slightly, then carefully slice it in half lengthwise and scoop out the seeds. Once cooled enough to handle, you can scrape out the strands and proceed with mixing the ricotta and sauce.
- **Instant Pot Method (efficient & hands-off):** The Instant Pot offers another excellent, hands-off approach. For this method, you’ll want to cut your spaghetti squash in half (either crosswise or lengthwise, depending on the size of your Instant Pot) and scoop out the seeds. Place the halves on the trivet with about a cup of water at the bottom of the pot. Set the Instant Pot to manual pressure cook for 7-8 minutes, followed by a quick release. Once depressurized, carefully remove the squash, and steam will have perfectly softened it, making it easy to scrape out the delicious strands.
Regardless of your cooking method, the key is to ensure the spaghetti squash is tender enough to easily separate into spaghetti-like strands with a fork. This provides the ideal base for our cheesy, flavorful filling.
Choosing and Preparing Your Spaghetti Squash
When selecting spaghetti squash, look for one that is firm, heavy for its size, and has no soft spots or blemishes. The skin should be a vibrant yellow or orange color. Preparing it can sometimes be a bit tricky due to its tough exterior. A sharp, sturdy chef’s knife is your best friend here. For safety, trim a small piece off one end to create a flat base, making it more stable on your cutting board before slicing it in half lengthwise.
Why Spaghetti Squash is a Low-Carb Superfood
Spaghetti squash is more than just a clever pasta substitute; it’s a nutritional powerhouse, especially for those mindful of their carbohydrate intake. It’s incredibly low in calories and carbohydrates compared to traditional pasta, making it perfect for keto, paleo, and gluten-free diets. Beyond its low-carb profile, spaghetti squash is a good source of fiber, which aids digestion and promotes a feeling of fullness. It also provides essential vitamins and minerals, including Vitamin C, Vitamin B6, niacin, and manganese. Its mild, slightly sweet flavor and unique texture make it a versatile vegetable that can truly elevate your healthy meal planning.
These Low Carb Spaghetti Squash Parmesan Boats are designed to be quite filling. Typically, one spaghetti squash will comfortably serve two people, offering a generous portion. However, if you’re serving lighter appetites or pairing it with a side dish, you can easily stretch one squash to serve three. And, as mentioned earlier, any leftovers are a treasure! They reheat beautifully, making for a convenient and delicious lunch the next day. So go ahead, make an extra batch and enjoy this wholesome, satisfying meal for days to come!

How to Make Cheesy Spaghetti Squash Boats
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Ingredients
- 2 small spaghetti squash – approx 1.5 lbs each, perfect for creating individual serving boats
- 2 tablespoons olive oil – for roasting and adding richness
- 1 tsp salt – to taste, enhances natural flavors
- 1 tsp pepper – freshly ground for best flavor
- ¾ cup whole milk ricotta cheese – creates a creamy, comforting filling
- 1 egg, whisked – acts as a binder for the filling
- 1 tablespoon Italian seasoning blend, dried – for authentic Italian flavor
- ¾ cup freshly grated Parmesan cheese – divided, for mixing into the filling and topping
- Rao’s Homestyle Italian Sausage & Mushroom Sauce – or your favorite low-carb marinara sauce, divided
- 6 ounces fresh mozzarella, thinly sliced or shredded – divided, for a gooey, melted topping
- fresh basil leaves, for garnish – optional, for a burst of freshness and color
Instructions
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Preheat your oven to 400°F (200°C). Carefully slice one end of each spaghetti squash off, then slice each squash in half lengthwise. Using a spoon, scoop out and discard all the seeds and fibrous strands from the center.
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Place the prepared squash halves, cut side up, on a parchment-lined rimmed baking sheet. Drizzle the cut sides generously with olive oil, then season evenly with salt and pepper. Flip the squash halves so they are cut side down, and roast in the preheated oven for 40-45 minutes, or until the flesh is easily pierced with a fork, indicating it’s tender.
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While the spaghetti squash is roasting, prepare your delicious filling. In a medium-sized bowl, combine the whole milk ricotta cheese, whisked egg, and Italian seasoning blend. Mix these ingredients thoroughly until well combined.
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Once the squash is cooked and slightly cooled, use a fork to gently scrape out the spaghetti-like strands from each half, leaving a thin border of squash inside the skin to maintain the “boat” shape. Transfer the scraped squash strands to the bowl containing the ricotta mixture. Stir in 1 cup of your chosen marinara sauce and half of the freshly grated Parmesan cheese (reserving the other half for topping). Mix until mostly combined but still slightly streaky, creating a beautiful texture.
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Carefully spoon the spaghetti squash and ricotta mixture back into the hollowed-out squash boats. Dollop additional marinara sauce over the top of the filling, then generously scatter with the fresh mozzarella slices or shreds. Finally, sprinkle with the remaining Parmesan cheese for an extra cheesy crust.
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Return the filled spaghetti squash boats to the oven and bake for another 20-25 minutes, or until the cheese is beautifully melted, bubbly, and browned in spots, indicating a perfect golden finish. If desired, garnish with fresh basil leaves before serving. Serve hot and enjoy this incredible low-carb comfort food!
Storage and Reheating Tips
These Cheesy Spaghetti Squash Boats make fantastic leftovers! To store, allow any remaining portions to cool completely, then cover tightly with plastic wrap or aluminum foil, or transfer to an airtight container. They will keep well in the refrigerator for up to 3-4 days. For reheating, you can either microwave individual portions for 2-3 minutes until heated through, or for a crispier top, reheat them in a preheated oven at 350°F (175°C) for about 15-20 minutes, or until warmed and the cheese is slightly re-crisped.
Delicious Variations and Add-Ins
Feel free to customize your spaghetti squash boats with your favorite ingredients:
- **Meats:** Add cooked ground beef, turkey, Italian sausage, or shredded chicken to the ricotta mixture for extra protein and flavor.
- **Vegetables:** Sautéed mushrooms, spinach (ensure it’s well-drained), bell peppers, or onions can be mixed into the filling.
- **Cheeses:** Experiment with different cheeses like provolone, fontina, or a blend of Italian cheeses for varying textures and tastes. A sprinkle of goat cheese could also add a tangy kick.
- **Spices:** Boost the flavor with a pinch of red pepper flakes for a bit of heat, or fresh herbs like oregano and thyme.
- **Sauce Alternatives:** While marinara is classic, you could also use a creamy alfredo sauce (ensure it’s low-carb if following keto) or even a pesto for a different flavor profile.
Serving Suggestions for a Complete Meal
These spaghetti squash boats are quite substantial on their own, but they pair wonderfully with a simple side to create a balanced meal. Consider serving them with a fresh green salad tossed in a light vinaigrette, some steamed green beans, or roasted asparagus. A side of garlic bread (or keto-friendly garlic bread for a low-carb option) would also be a delicious accompaniment.

I hope you absolutely love these Cheesy Spaghetti Squash Boats as much as my family and I do! They truly embody the perfect balance of wholesome nutrition and indulgent comfort. Don’t forget to share your creations with us online!
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