5 from 4 votes
Overhead photo of Pesto Spaghetti Squash Casserole garnished with fresh basil in a white baking dish with serving spoons inserted into the casserole and a ramekin of grated parmesan and a pale tan napkin next to the dish.
Pesto Spaghetti Squash Casserole
Prep Time
20 mins
Cook Time
1 hr 5 mins
Total Time
1 hr 25 mins

This Pesto Spaghetti Squash Casserole is an easy, healthier version of lasagna!  Spaghetti squash is layered with pesto ricotta, mozzarella and marinara.  This spaghetti bake is budget-friendly, simple to prepare and a meal the entire family will love!

Recipe can be scaled up or down by using the slider if you hover your mouse over the number of Servings.

Course: entree, main
Cuisine: American, Italian
Keyword: Casserole, Healthy, lasagna, pesto, spaghetti, squash
Servings: 8
Calories: 290 kcal
  • 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
  • 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 – Homemade or Store bought
  • 1 clove Garlic – finely chopped
  • 2/3 Cup Freshly Grated Parmesan Cheese - DIVIDED
  • 8 ounces Fresh Mozzarella – torn or shredded
  1. Roast the spaghetti squash: Heat 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. 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.

  2. While the spaghetti 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. Set aside.

  3. Add flavor to your marinara: Stir fresh basil into your marinara sauce. Taste. Adjust your sauce to taste with salt and pepper. Set aside.

  4. Assemble the casserole: Grease 9x13-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.

  5. Bake: Bake in the oven (preheated to 400 degrees F) for 25-30 minutes or until the top of the casserole is browned and bubbly.

  6. Serve: Let cool 10 minutes before serving. Garnish with more parmesan cheese and fresh basil if desired. Enjoy!

Recipe Notes
  1. 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!

To make your own spaghetti sauce:  (Yield 3 Cups)

2 TBS Olive Oil

1 small Yellow Onion – finely diced

3 cloves Garlic – chopped

1 tsp EACH: Smoked Paprika & Dried Oregano

1 TBS Tomato Paste

1 (28 ounce) Can Peeled, Whole San Marzano Tomatoes – crushed by hand

  1. Heat oil in a medium saucepot over medium heat. When the oil shimmers, add the onions and season with salt and pepper. Cook, stirring occasionally, for 5 minutes or until the onion are softened. Add in the garlic, paprika and oregano. Cook, stirring, until fragrant, about 30 seconds. Add in the tomato paste and cook, stirring, until the tomato paste starts to caramelize, about 1-2 minutes. Add in the tomatoes and season with salt and pepper.
  2. Bring to a rapid simmer and then immediately reduce to a gentle simmer. Cook, stirring occasionally, for 40-45 minutes, or until sauce is thick. (Stir in basil from recipe above). Taste and adjust for seasoning. Remove from heat and set aside.

Recipe serves: 6-8

Nutritional information is an approximation and based upon 8 servings.

Nutrition Facts
Pesto Spaghetti Squash Casserole
Amount Per Serving
Calories 290 Calories from Fat 171
% Daily Value*
Fat 19g29%
Saturated Fat 10g63%
Cholesterol 61mg20%
Sodium 859mg37%
Potassium 531mg15%
Carbohydrates 16g5%
Fiber 3g13%
Sugar 8g9%
Protein 17g34%
Vitamin A 1098IU22%
Vitamin C 9mg11%
Calcium 404mg40%
Iron 2mg11%
* Percent Daily Values are based on a 2000 calorie diet.