Cheesy Baked Spaghetti Squash with Pesto

I know what you’re thinking… What’s so special about spaghetti squash? I may be the first to say it, but it’s completely underrated. It’s cauliflower’s less popular cousin but oh so good and easy to cook. 

I think people are afraid to eat it because they think it might be gross or don’t know how to cook it. I love spaghetti squash in a way that’s almost judge-worthy. Yes, it’s a bit higher in carbs but worth it. It’s incredibly versatile too.

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Is spaghetti squash keto?

Spaghetti squash is a type of winter squash that is low in calories and carbs, but rich in vitamins, dietary fiber, manganese, magnesium, potassium, omega-3s, and omega-6s.

One cup of spaghetti squash is 8 net carbs. It’s net carb count is line with other healthy veggies like eggplants or Brussels sprouts

Unlike other winter squash varieties, its long strands make it the perfect choice as a low-carb pasta alternative.

Spaghetti Squash nutrition information per 1 Cup:

  • Calories: 42
  • Fat: 0.4g
  • Carbohydrates: 10g
  • Fiber: 2.2g
  • Sugar: 3.9g
  • Protein: 1g

Source: USDA

To pick the best one, you need to know how to tell if spaghetti squash is ripe. 

The more yellow the squash, the riper it is! Uncooked squash doesn’t need to be refrigerated until after you cut/cook them. If you’re taking a chance with Instacart, your best bet is to ask for a very yellow squash.

spaghetti squash
Forest & Kim Starr, CC BY 3.0, via Wikimedia Commons

How to cook spaghetti squash

This squash looks intimidating, but it’s super easy. You can cook spaghetti squash in an air fryer, put it in the Instant Pot, or bake it in the oven. 

For the air fryer and oven, poke the squash with a knife several times before placing it in the microwave on high for about 5 minutes. If it’s a big squash you may need to nuke it for another couple of minutes until it’s easy to cut.

Once you remove it from the microwave (be careful, it will be hot!) place it on a cookie sheet lined with parchment paper or a silicone baking mat. There are a million ways to make it, but the standard is slice, scoop, bake.

Slice the squash lengthwise. I haven’t tried it, but if you want to get wild, cut it horizontally (Like a madman)

Once you cut it, scoop out the seeds and pulp like you would with a pumpkin, drizzle with a keto friendly oil like olive or avocado, and season with a bit of salt. Place the sliced squash face down if going in the oven, or face-up if placing in the air fryer and roast that squash.

When it’s done, scrape it with a fork to get that noodle appearance. This squash is the best noodle replacement in my opinion if you’re trying to keep it clean.

I love to eat it plain, or covered in sauce and cheese. I needed to find some fresh spaghetti squash recipes because the hubs has been judging my squash habit. After enjoying it many times as a noodle sub, I thought about how I could make it a glorious side dish and BOOM….

Cheesy Baked Spaghetti Squash with Pesto

This is a single serving, but feel free to make a whole batch. I would have eaten half a squash but the husband was judging watching. This is a great recipe to use up any leftover squash you may have.

Cheesy Keto Baked Spaghetti Squash with Pesto

Prep Time: 10 minutes
Cook Time: 45 minutes
Course: Side Dish
Cuisine: American
Keyword: pesto, spaghetti squash
Servings: 1
Author: Kari Hale


  • 6 oz Cooked spaghetti squash
  • 2 tbsp Pesto sauce
  • 1 oz Mozzarella Fresh or shredded


Cook the Spaghetti Squash

  • Poke holes into the spaghetti squash with a fork or knife
  • Microwave on high for 5-7 minutes
  • Cut squash in half and scoop out seeds and pulp
  • Drizzle with oil (Olive or Avocado) and season with salt and pepper
  • Place flat side down on cookie sheet (Or face up in air fryer)
  • Bake for 30 minutes

Cheesy Baked Spaghetti Squash and Pesto

  • Place 6oz of cooked spaghetti squash in a Pyrex dish layered with Pesto on top and sprinkled with the mozzarella.
  • Put in air-fryer (or oven) for about 5 minutes at 390 degrees until cheese is melted and golden brown.
Tried this recipe?Let us know how it was!

I love the buttery flavor of this squash. The texture won’t truly replace that of carby pasta, but I don’t find myself missing pasta like I used to. 

So go pick out a spaghetti squash, you’ve never adulted harder. If you make this spaghetti squash bake, let me know what you think!

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