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If you’re looking for a veggie-packed twist on comfort food, look no further than this mouthwatering masterpiece—Pesto Spaghetti Squash. This Italian-inspired recipe combines tender spaghetti-like strands of squash with herbaceous pesto sauce, rich marinara, and three types of cheeses. Simple to prepare with 8 basic ingredients, this casserole is equal parts indulgent and deliciously wholesome.

“I made this last tonight! I’m a lasagna fanatic, and this pesto with spaghetti squash version is delicious! You’re a genius!”

– KAYLA
Overhead photo of pesto and spaghetti squash casserole with basil ricotta and mozzarella.

Update: This recipe was originally published in January 2020. I made edits to the article below to include more information about making this spaghetti squash casserole with pesto at home. 

Hi, friends! If you love lasagna and spaghetti casseroles, it’s my pleasure to introduce you to today’s dish, which will surely have you saying “Mamma Mia” with every single bite:

Table of Contents

About this pesto spaghetti squash

With the ideal combination of satisfying textures and deliciously cozy, vibrant flavors, this pesto spaghetti squash casserole will have everyone reaching for seconds.

Picture this: delicate strands of spaghetti squash layered with creamy basil pesto sauce infused ricotta, rich tomato marinara sauce, melty mozzarella, and freshly grated parmesan cheese. Finished with a generous sprinkling of fresh sweet basil and more cheese, this pesto with spaghetti squash is robust and rich in flavor – and also lower in carbs than the traditional Italian dish.

And the best part (aside from the taste)? This recipe is super simple to prepare with just 8 ingredients and 20 minutes of hands on preparation.

Whether you’re hosting a dinner party or simply looking to feed your family a vegetable-packed, deliciously cozy meal, this spaghetti squash with pesto sauce is feast for your eyes AND your tastebuds!

Why you’ll love this recipe!

There’s so much to love about this pesto spaghetti squash recipe:

  • Simple to Make with Easy-to-Find Ingredients. This recipe relies on simple ingredients and straightforward steps to ensure dinner success.
  • Wholesome yet Super Satisfying. Swapping out classic noodles for spaghetti squash ensures this pesto and spaghetti squash casserole is the ideal mix of savory, hearty, and light.
  • Cozy and Flavorful. Silky spaghetti squash meets vibrant pesto, creamy ricotta, and plenty of melty cheese.
  • Customizable. This spaghetti squash recipe is incredibly easy to customize to suit your taste preferences and/or whatever you have on hand. Add more garlic, swap the mozzarella for burrata, nix the basil pesto in favor of tomato pesto, and so on.
  • All Season Recipe. While the fresh basil and pesto are perfect for summer, the spaghetti squash works great in winter and fall—ensuring you can get your comfort food fix regardless of the season.
Overhead photo of spaghetti squash strands in a roasted half of spaghetti squash.

Ingredients for spaghetti squash pesto

  • Spaghetti Squash. This yellow squash is the star of the show, so be sure to look for one that’s firm with smooth, yellow skin for the best flavor.
  • Marinara Sauce. Make sure to use a good-quality brand of red tomato sauce or make your own marinara sauce for the best flavor.
  • Fresh Basil. Vibrant with a delightful aroma, basil leaves lend a slightly peppery flavor and subtle fresh sweetness.
  • Ricotta Cheese. Grab whole milk ricotta cheese for the best texture.
  • Basil Pesto Sauce. You can use homemade basil pesto sauce or store-bought, depending upon your preference.
  • Garlic. Fresh garlic lends a subtle punch of irresistible flavor. Be sure you use fresh cloves of garlic and mince them yourself for the best flavor. That minced stuff in a jar is convenient, but it definitely lacks the same flavor as the fresh stuff.
  • Parmesan Cheese.  Freshly grated parmesan cheese lends a salty, slightly nutty finish.
  • Mozzarella Cheese. Fresh mozzarella lends richness and the perfect touch of cheesy indulgence. Swap: You can use burrata if you’re looking for even more richness.

Recipe variations

If you’ve got leftover pesto sauce, put it to good use in these delicious recipes next: Pesto Sausage and Veggies, Tortellini Pesto, and Arugula Pasta Recipe.

Overhead photo of spaghetti squash strands layered with pesto sauce, marinara, and cheeses in a casserole dish - before baking.

How to make spaghetti squash with Pesto sauce

This recipe for pesto spaghetti squash is extremely easy to make with 20 minutes of hands on preparation. Here’s how:

  1. Roast the spaghetti squash: Rub the cut sides of the squash with olive oil and season to taste with salt and pepper. Then roast the squash in a 400-degree oven until it’s fork tender. Once it’s cool enough to handle, use a fork to gently scrape out the strands of squash and discard squash “shells”. Working in batches, transfer the squash “noodles” to a kitchen towel or tea towel and squeeze to remove the excess water from the squash. Transfer the strands of squash to a bowl and set aside.
  2. Make the pesto ricotta mixture: In a medium bowl, combine the ricotta with the pesto, garlic, and parmesan cheese, salt, and black pepper. Then, stir to combine and set the pesto mixture aside.
  3. Add flavor to your marinara:  Stir fresh basil into your marinara sauce. Then taste it and adjust your sauce with salt and pepper.
  4. Layer spaghetti squash with pesto and marinara: Grease a 9×13-inch casserole dish. Spread a thin layer of tomato sauce onto the bottom of the dish. Top with half of the spaghetti squash noodles. Then, top with half of the ricotta mixture. Next, layer on half of the remaining tomato sauce and half of the mozzarella cheese. Repeat with the remaining squash noodles, ricotta and tomato sauce. Finally, sprinkle with the rest of the mozzarella and parmesan cheeses.
  5. Bake: Place the spaghetti squash pesto casserole into the oven and bake for 25-30 minutes or until the top of the casserole is bubbly.
  6. Serve: Let cool for 10 minutes before garnishing with cheese and basil. Serve pesto spaghetti squash casserole and enjoy.

Chef expert tips for perfect results every time!

  • Choose the Best Squash. Since spaghetti squash is the main ingredient, you’ll want to be sure to grab a good looking one at the grocery store. When shopping, select a squash that feels heavy for its size with deep yellow coloring and a hard exterior.
  • Use Good-Quality Sauces. The pesto sauce and tomato sauce are pretty key ingredients in this recipe, so make sure you use high-quality brands or use homemade for the best taste.
  • Roast the Spaghetti Squash Until Tender. To get perfectly tender spaghetti-like strands of squash, roast the squash until the flesh is soft and it easily separates into strands when you scrape it with the tins of a fork.
  • Drain Well. Spaghetti squash is a watery vegetable. Make sure you squeeze the spaghetti squash strands dry using a kitchen towel or paper towels before assembling the casserole in the baking dish.
  • Garnish Before Serving. Garnishes are more than just decorative flare – they can take your final dish from ho-hum to oh-yum – so consider finishing your pesto squash with a generous dusting of parmesan, fresh basil leaves, ground black pepper, and crushed red pepper flakes before serving.

Step-by-step photos: making this recipe at home 

If you’re looking for the detailed measurements and full recipe instructions, please scroll down to the bottom of the page. 

Overhead photo collage of how to make Pesto Spaghetti Squash Casserole step by step with the written instructions written out on each photo.

FAQs: frequently asked questions

You’ve got questions? I’ve got answers! If you have a question you don’t see listed below, please drop them in the comments section. I’m happy to help when I can! 

What is spaghetti squash casserole?

Spaghetti squash casserole is an easy and healthier version of hearty classic spaghetti casserole. A flavorful tomato sauce is layered with cooked spaghetti squash and cheese, and then baked in the oven until hot and bubbly. Squash casserole can be made with meat sauce or plain tomato sauce for vegetarians.

Can I use store-bought pesto?

Absolutely! You can use homemade or store-bought basil pesto sauce here – just make sure to select a good-quality brand if using store-bought.

How to cut a whole spaghetti squash?

Spaghetti squash needs to be cut into two halves before baking or roasting.

  1. Spaghetti squash has a very tough exterior, so I recommend using a sharp paring knife to make small incisions, lengthwise, along the side of the squash where you plan to cut it.
  2. Microwave the squash for 3-5 minutes to help soften the exterior before cutting. Allow the squash to cool until no longer hot to the touch.
  3. Place squash on a clean work surface and use a sharp knife to cut the squash lengthwise, from the top to the base, along the same line of incisions you made previously.
  4. Use a large spoon or ice cream scoop to scoop out the seeds and discard them before baking.

How do I know when the spaghetti squash is done cooking?

Spaghetti squash is done roasting in the oven when the flesh easily separates into spaghetti-like strands when you scrape it with a fork.

Tips for perfectly roasted spaghetti squash:

  • Bake the squash at moderately high heat (400 degrees F) for the most flavorful, slightly caramelized strands of squash.
  • Avoid roasting cut side up or water will pool inside the squash.
  • Check the squash for doneness. Smaller spaghetti squash will take around 30 minutes, while large squash can take up to 55 minutes.

How to prevent watery spaghetti squash casserole?

While spaghetti squash is a wonderful alternative to pasta, isn’t an actual replacement or true substitution for pasta. Spaghetti squash has a tendency to get a bad reputation because it does release water when cooked.

To prevent watery spaghetti squash, it is imperative you place the cooked strands of spaghetti squash in a kitchen or tea towel and squeeze out the excess water before proceeding with assembling the casserole. Also, make sure you are properly cooking the spaghetti squash (as noted above).

Action photo a serving spoon digging into a casserole made with pesto, spaghetti squash, marinara, ricotta, and mozzarella.

Serving suggestions for pesto and spaghetti squash

Common serving suggestions

Unique serving ideas

Storing leftovers

Storage instructions

  • Allow any leftover spaghetti squash and pesto to cool completely to room temperature.
  • Store leftovers in an airtight container in the fridge for up to 4 days.

Freezing instructions

You can freeze this recipe for pesto spaghetti squash one of two ways – before or after baking:

  • To freeze the casserole before baking:  Prepare and assemble the squash casserole according to the recipe instructions. Make sure you assemble the casserole in a dish that can go straight from the freezer into a hot oven (avoid ceramic, porcelain or glass baking dishes). Cover the dish with a lid or a layer of plastic wrap followed by a layer of aluminum foil. The unbaked casserole can be stored in the freezer for up to 3 months.
  • To freeze a leftover baked casserole:  Prepare, assemble and bake the casserole according to the instructions in the recipe. Allow the dish to come to room temperature before wrapping with a layer of plastic wrap and then a layer of aluminum foil. The baked casserole can be stored in the freezer for up to 3 months.

Reheating instructions

  • Reheating unbaked casserole: Uncover the spaghetti squash casserole and transfer the frozen casserole directly to an oven preheated to 350 degrees. Bake for 45 minutes, or until warmed throughout.
  • For reheating leftovers: Defrost the casserole in the refrigerator overnight if frozen.
    • To reheat in the oven:  When ready to eat, reheat in an oven preheated to 350 degrees F. Bake until heated throughout.
    • To reheat in the microwave:  Alternatively, (defrosted) leftovers can be reheated in the microwave until warmed throughout! Microwave individual servings of casserole at 50% power for 1-3 minutes, or until warmed throughout.
  • Pro-Tip: If you are using a glass baking dish, make sure you let the casserole sit on the counter and come to room temperature before placing in the oven. Glass can easily crack and shatter if the temperature changes from cold to hot too quickly!
  • Cook’s Note: Spaghetti squash does release water when reheated, however the water won’t hurt anything!
Close-up photo of spoons serving spaghetti squash with pesto sauce from a baking dish.

Until next week, friends, cheers – to better comfort food!

Cheyanne

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More spaghetti squash recipes!

Overhead photo of pesto spaghetti squash with two serving spoons inserted into the casserole dish.

Pesto Spaghetti Squash

5 from 2 votes
Author: Cheyanne Holzworth
Total Time: 1 hour 25 minutes
Prep Time: 20 minutes
Cook Time: 1 hour 5 minutes
Servings: 8 servings
Print Recipe Pin Recipe
If you're looking for a veggie-packed twist on comfort food, look no further than this mouthwatering masterpiece—Pesto Spaghetti Squash. This Italian-inspired recipe combines tender spaghetti-like strands of squash with herbaceous pesto sauce, rich marinara, and three types of cheeses. Simple to prepare with 8 basic ingredients, this casserole is equal parts indulgent and deliciously wholesome.

Equipment

  • 1 Rimmed Baking Sheet
  • 2 Medium Mixing Bowls
  • 1 9×13-inch Casserole Dish

Ingredients 

  • 1 large Spaghetti Squash (about 4 to 4 ½ pounds) – halved lengthwise and seeds removed (SEE NOTES)
  • 1-2 TBS Extra Virgin Olive Oil – to taste
  • to taste Kosher Salt & Ground Black Pepper
  • 3 Cups Thick Marinara Sauce (SEE NOTES)
  • ¼ Cup Fresh Basil Leaves – thinly sliced, plus more for garnish
  • 2 Cups Whole Milk Ricotta Cheese
  • ½ heaping Cup Basil Pesto Sauce – homemade or store-bought
  • 1 clove Garlic – finely chopped
  • 2/3 Cup Freshly Grated Parmesan Cheese – DIVIDED
  • 8 ounces Fresh Mozzarella – torn or shredded

Instructions

  • Roast the Spaghetti Squash: Arrange oven rack to the center position and then preheat the oven to 400 degrees F.
    Line a rimmed baking sheet with parchment paper for easy clean up.
    Rub the cut sides of the squash with olive oil and season to taste with salt and pepper. And then place the squash, cut side down, on the prepared baking sheet.
    Transfer to the oven and bake for 40-50 minutes, or until the squash is tender and easily pierced with a fork.
    When squash is cooked and cool enough to handle, use a fork to gently scrape out the strands of squash and discard squash “shells”.
    Transfer the squash strands, in batches, to a kitchen towel or tea towel. Squeeze the excess water out of the spaghetti squash.
    Transfer to a bowl and set aside. Keep the oven at 400 degrees F.
  • While the Squash Roasts, Make the Pesto Ricotta Mixture: In a medium bowl, combine the ricotta with the pesto, garlic, and 1/3 cup parmesan cheese. Season with ¼ teaspoon salt and 1/8 teaspoon ground black pepper. Stir to combine and then set the bowl aside.
  • Flavor the Marinara Sauce: Stir the fresh basil into your marinara sauce. Give the sauce a taste and adjust it to suit your tastebuds. Then set it aside.
  • Layer the Spaghetti Squash with Pesto, Marinara, and Cheese: Grease 9×13-inch casserole dish.
    Spread ¾ cup of the tomato sauce onto the bottom of the dish.
    Top with half of the cooked spaghetti squash noodles. Top with half (1 ½ cups) of the ricotta mixture followed by half (1 ¼ cups) of the remaining tomato sauce and half (4 ounces) of the mozzarella cheese.
    Repeat with the remaining squash noodles, ricotta and tomato sauce.
    Sprinkle with remaining mozzarella cheese and remaining 1/3 cup parmesan cheese.
  • Bake Pesto Spaghetti Squash in Oven: Transfer the casserole to the preheated oven and bake for 25-30 minutes or until the top of the casserole is browned and bubbly.
    Remove from oven and place the casserole dish onto a wire rack. Let cool for 5-10 minutes before garnishing and serving.
  • Serve Pesto Spaghetti Squash Casserole: Garnish the top of the spaghetti squash with more parmesan cheese and fresh basil, if using. Enjoy immediately.

Notes

  1. Squash: You can use one large spaghetti squash or two smaller ones. Just make sure overall your squash measures roughly 4 to 4 ½ pounds. If you meal prep and have cooked spaghetti squash on hand, the equivalent is about 9 cups of cooked spaghetti squash strands.
  2. To make the squash easier to cut in half: Use the tins of a fork to poke the outside of the squash a few times. Place the squash on a microwave safe plate and microwave on high for 3-5 minutes to soften the exterior before cutting.
  3. If you like things spicy, add a teaspoon of crushed red pepper flakes to your marinara sauce. 
  4. Need protein?  Feel free to add cooked, shredded chicken, turkey, ground beef or ground pork to the casserole! Or, if you prefer meat, try making this with homemade Bolognese instead of the tomato sauce.
  5. Gluten-free?  Make sure your marinara sauce is gluten-free.
  6. Need to Scale the Recipe? Hover your mouse over the number of servings in the recipe card. You’ll see a sliding scale pop up, you can use that to scale the recipe up or down as needed.
  7. Got questions? I’ve got answers! If you ever run into an issue, have a question, or need any clarification – please feel free to drop them in the comments section. I’m happy to help when I can! 
Nutritional information is provided as a courtesy and the nutrition facts are an estimate based upon 8 servings. Exact information will depend upon the brands of ingredients and precise measurements used.

Nutrition

Calories: 291kcal    Carbohydrates: 16g    Protein: 17g    Fat: 19g    Saturated Fat: 10g    Polyunsaturated Fat: 1g    Monounsaturated Fat: 6g    Cholesterol: 61mg    Sodium: 814mg    Potassium: 504mg    Fiber: 3g    Sugar: 7g    Vitamin A: 1101IU    Vitamin C: 9mg    Calcium: 407mg    Iron: 2mg
Course: entree
Cuisine: Italian

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