Looking for a comforting, healthy, and tasty baked spaghetti squash recipe that’s easy to make? Look no further! This stuffed spaghetti squash is filled with cannellini beans, sweet cherry tomatoes, onion, garlic, and baby spinach combined with a delicious almond pesto sauce. It's vegan, gluten-free, oil-free, soy-free, and a winner all the way around!

Half of a stuffed spaghetti squash topped with fresh basil on a plate with two forks.

This recipe makes two generous servings or four smaller dinner portions.

Why This Baked Spaghetti Squash is a Winner

Easy to Make: While the spaghetti squash is baking in the oven, you can easily prepare the stuffing on the stovetop.
Packed with Nutrients: Full of fiber, protein, vitamins, minerals, and healthy plant fats.
Meal Prep Friendly: Make the components ahead of time for a quick meal during the work week.
Satisfying: This meal is comforting without leaving you feeling heavy.

What You Need to Make This Spaghetti Squash Recipe

Spaghetti squash
Vegan almond pesto
Cannellini beans
Onion
Garlic
Spinach
Cherry or grape tomatoes
Oregano
Crushed red pepper flakes
Low-sodium vegetable broth

Ingredients for stuffed spaghetti squash: spaghetti squash, vegan almond pesto, spinach, cherry tomatoes, onion, garlic, cannellini beans and seasonings.

How to Prepare

1. Roast the Spaghetti Squash

Preheat your oven to 400°F (205°C).

Cut the spaghetti squash in half lengthwise and scoop out the seeds. Place them cut-side down on a baking sheet lined with parchment paper.

Roast 30-35 minutes or until the flesh is tender and easily separates into strands with a fork. Set aside.

Spaghetti squash cut in half lengthwise and placed on a parchment lined baking sheet in the oven. — After slicing and removing seeds, turn the spaghetti squash cut side down on a parchment-lined baking sheet and bake in a preheated 400F (205C) oven for 30 to 35 minutes.

Two halves of a spaghetti squash that have been baked. — Removed cooked spaghetti squash from the oven and carefully turn it over to cut side up to cool slightly.

2. Make the Pesto

While the spaghetti squash is baking in the oven, prepare the 5-minute vegan almond pesto according to recipe instructions. Set aside.

3. Cook the Filling

Heat a skillet over medium heat. Add the chopped onion and cherry tomatoes, put the lid on, and cook for 3 to 4 minutes.

Add half the low-sodium vegetable broth, garlic, oregano, crushed red pepper and cannellini beans. Stir to incorporate and put the lid back on to continue cooking for 3 to 4 minutes. The cherry tomatoes should start to break down.

Add the remaining vegetable broth and spinach. Give it a good stir to incorporate, and put the lid on. Continue cooking for another 2 minutes or until spinach wilts. If beans and veggies start to stick, add more vegetable broth or water.

Turn off the heat and fold in the vegan almond pesto until all the veggies and beans are coated in the pesto deliciousness. Salt and pepper to taste.

Chopped onions and tomatoes in a sauté pan with a lid being put on top. — Heat a skillet over medium heat. Add the chopped onion and cherry tomatoes, put the lid on, and cook for 3 to 4 minutes.

Beans, seasonings, tomatoes, onions and veggie broth in a pan with wooden spoon stirring. — Add half the low-sodium vegetable broth, garlic, oregano, crushed red pepper and cannellini beans. Stir to incorporate.

Beans, cherry tomatoes, and veggies that have been cooked down in a pan. — Put the lid back on to continue cooking for 3 to 4 minutes. The tomatoes should break down.

Spinach added to the pan with beans and other veggies and a woman's hand putting a lid on top. — Stir in the spinach and put the lid back on to continue cooking for another 2 minutes.

Almond pesto being dolloped on top of the pan with beans and veggies. — Turn off the heat and dollop the vegan almond pesto sauce onto the hot veggies and beans.

Spaghetti squash filling of beans and veggies being coated with pesto sauce in the pan. — Fold in the pesto until veggies and beans are well coated.

4. Stuff the Spaghetti Squash

Using a fork, scrape the roasted spaghetti squash into strands while keeping the shells intact. Fill the squash shells with the filling.

A woman using a fork to shred the baked spaghetti squash.

If you're dividing this into four smaller dinner portions, feel free to scoop the spaghetti squash strands onto a plate and dollop a generous amount of the stuffing.

5. Serve!

Optional: Return the stuffed squash halves to the oven and bake for 5 to 7 minutes at 375°F (190°C) to heat through.

Serve warm and top with extra basil or vegan parmesan cheese if desired.

Vegan spaghetti squash on a plate with stuffing mixture of white beans, spinach, tomatoes, vegan almond pesto, and seasonings.

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Tips

Customize the Filling: Add your favorite veggies like zucchini or mushrooms, or substitute cannellini beans for butter beans.
Make Ahead: Roast the squash and make the filling up to 3 days in advance. Store separately and assemble before serving.
Storage: Leftovers can be stored in an airtight container in the fridge for up to 4 days.

Nutritional Benefits of This Spaghetti Squash Recipe

Spaghetti Squash: This is a low-calorie pasta alternative rich in vitamins A and C.
Cannellini Beans: Protein and fiber to keep you full. Beans have numerous health benefits—from reducing heart disease to weight management and blood sugar control.
Spinach: Rich in Vitamins A, C, and K, as well as iron, calcium, and antioxidants. Spinach is associated with improved heart health and reduced inflammation.
Basil Almond Pesto: The almonds in this pesto have several health benefits, including supporting heart health. Basil adds a fantastic flavor to this dish, as well as nutrients like Vitamins A and K, and other beneficial compounds.

This vegan stuffed spaghetti squash is a textural and flavorful winner. Whether you’re cooking for one or a family, it’s a showstopper. If you try, we'd love to hear how it went and if you made any modifications. Please leave a review below.

Gigi & Sersie

May 03, 2025 at 3:37 am

Delicious! The spaghetti squash keeps it light, and the meatiness of the butter beans gives it a heartiness. The almond pesto ties everything together. So yummy.

Stuffed Spaghetti Squash

Why This Baked Spaghetti Squash is a Winner

What You Need to Make This Spaghetti Squash Recipe