This Stuffed Spaghetti Squash recipe is easy to make with fresh veggies and dairy-free cheese and makes the perfect low carb vegan meal! A healthy, hearty and delicious dinner that is gluten-free, low carb and keto-friendly.
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Veggie Stuffed Spaghetti Squash Recipe
Spaghetti squash season is in full swing and one of our favorite ways to enjoy it is roasting it in the oven with a delicious filling. This Stuffed Spaghetti Squash is perfect when you’re craving healthy comfort food and makes the perfect low carb pasta alternative. The great thing about spaghetti squash is that the taste is pretty neutral so it goes well with pretty much any veggies and sauce you add.
Ingredients you need
- Medium Spaghetti Squash
- Broccoli
- Zucchini
- Grated carrots
- Salt + black pepper, to taste
- Italian seasoning – or make your own with a mix of basil, oregano and thyme
- Marinara sauce – we like Rao’s for the taste and ingredients but you can use any tomato sauce you like or have on hand
- Vegan mozzarella – we like Miyokos but you can also sub with regular cheese if not dairy-free
- Parsley
- Optional: Grated parmesan OR nutritional yeast
How to make Stuffed Spaghetti Squash
- Preheat oven to 400F.
- CUT THE SPAGHETTI SQUASH: Cut the spaghetti squash in half lengthwise and scoop out the seeds. (For easier cutting, microwave the squash for 5 minutes on high in the microwave.)
- SEASON SQUASH AND BAKE: Brush or drizzle the cut sides with oil. Season with 1/3 tsp salt and 1/4 tsp black pepper. Place the squash cut-side down in a baking pan or on a rimmed baking sheet.
Roast for 35-45 minutes or until tender and easily pierced with a fork. (Cooking time will vary depending on the size of the squash). - COOK THE VEGETABLES: While the squash is roating, steam blanch or saute the broccoli, zucchini and carrots in a medium pot for a few minutes until tender. Season with Italian seasoning and salt and pepper, to taste. Add the marinara sauce and stir in 1/4 cup of mozzarella cheese. Remove from heat.
- ASSEMBLE SQUASH BOWLS: Once the squash is tender, remove from the oven and carefully flip each bowl over. Use a fork to scrape up some of the squash strands to fluff it up.
Fill each squash bowl evenly with the marinara / veggie filling. Top with remaining mozzarella and grated parmesan. - BAKE AGAIN: Bake at 350 F for around 10-15 minutes, until cheese is melted and filling is hot.
- GARNISH AND SERVE: Garnish with parsley and enjoy warm
Storage and freezer instructions
How to store stuffed spaghetti squash: To store the leftovers of this keto spaghetti squash, place in a sealed air tight container in your fridge for up to 4 days.
How to freeze stuffed spaghetti squash: The great thing about vegan stuffed spaghetti squash is that you can freeze leftovers in a sealed air tight container for up to 3 months.
To reheat – Remove spaghetti squash from freezer and reheat spaghetti squash leftovers in the microwave for 2 minutes or bake in your oven or toaster oven until heated through.
What to serve spaghetti squash with
Spaghetti squash noodles can be used in any recipe in place of pasta! In the cooler October fall weather, we love serving ours with Instant Pot Lemon Chicken with Garlic and Meatballs. And in the warmer summer months, the stuffed squash boats go perfectly with a side of Spinach Salad or Grilled Zucchini.
More spaghetti squash recipes you will love:
Chicken Parmesan Spaghetti Squash Bowls

This Stuffed Spaghetti Squash recipe is easy to make with fresh veggies and makes the perfect low carb vegan meal! A healthy, hearty and delicious dinner that is gluten-free and paleo-friendly!
- 1 medium spaghetti squash , cut in half with seeds removed
- 1/2 tbsp avocado oil OR olive oil
- 2 cups chopped broccoli florets
- 1 medium zucchini , chopped
- 1/4 cup grated carrots
- 1/2 tsp Italian seasoning , or use a mix of oregano, basil, thyme
- 1/2 cup Marinara sauce , we like Rao's
- Sea salt and black pepper , to taste
- 1/2 cup shredded vegan mozzarella cheese , divided (can sub with regular cheese if not dairy-free or paleo)
- 2 tbsp grated vegan parmesan , (can sub with regular cheese if not dairy-free or paleo)
- Chopped parsley to garnish
Preheat oven to 400F.
Cut the spaghetti squash in half lengthwise and scoop out the seeds. (For easier cutting, microwave the squash for 5 minutes on high in the microwave.)
Slice the spaghetti squash in half lengthwise and scrape out the seeds. Brush or drizzle the cut sides with oil. Season with 1/3 tsp salt and 1/4 tsp black pepper. Place the squash cut-side down in a baking pan or on a rimmed baking sheet.
Roast for 35-45 minutes or until tender and easily pierced with a fork. (Cooking time will vary depending on the size of the squash).
While the squash is roating, steam blanch or saute the broccoli, zucchini and carrots in a medium pot for a few minutes until tender. Season with Italian seasoning and salt and pepper, to taste. Add the marinara sauce and stir in 1/4 cup of mozzarella cheese.Remove from heat.
Once the squash is tender, remove from the oven and carefully flip each bowl over. Use a fork to scrape up some of the squash to fluff it up.
Fill each squash bowl evenly with the marinara / veggie filling.
Top with remaining mozzarella and grated parmesan. Bake at 350 F for around 10-15 minutes or until hot and bubbly.
Garnish with parsley and enjoy warm.
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