Gluten Free/ Low Carb/ Main Dishes/ Vegetarian

Baked Spaghetti Squash with Cheesy Chipotle

baked spaghetti squash

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This baked spaghetti squash recipe is a low carb cheesy and spicy comfort dish that can be served as a hearty main or a side dish.

The slight spicy heat of the chipotle pepper gives the spaghetti squash a touch of flavour and goes well with the cheese too. If you serve it as a side dish, you could scoop the baked spaghetti squash out directly onto your dinner plate. For dinner parties or holiday meals, serve it in it’s case for a nicer presentation.

spaghetti squash with a cheesy chipolte filling

Keto Spaghetti Squash Recipe

I’ve baked this cheesy chipotle spagehetti squash a few times and love it time. The Chief Taster complained about the cream cheese as he prefers his cream cheese in a cheesecake rather than a savoury dish. If you have the same complaint, replace the cream cheese with Cheddar cheese.

For me, the chipotle pepper lifts what could be a bland dish to a recipe with flavour. I used chipotle chilli from a can, so I can use a bit of the sauce for extra taste. Combined with the cheese it is delicious.

Carbs in Spaghetti Squash

Spaghetti squash is suitable for low carb diets as well as being low in calories and high in fibre. It’s spaghetti-like flesh is a great pasta replacement and can be served simply by itself or with a sauce.

With only 10 grams total carbs per one-cup serving this squash makes a great low carb alternative to wheat spaghetti, as well as being a deliciously healthy gluten free option.

baked spaghetti squash


For speed I first cook this squash in the microwave before being filled and baked in the oven. Although you can bake the spaghetti squash in the oven first it is quicker to cook it in the microwave. Baking it would take about 30-40 minutes whereas the microwave takes 15 minutes.


chipolte spaghetti squash

Baked Spaghetti Squash with Cheesy Chipotle

Spaghetti squash baked with a cheesy chipolte filling for a low carb comfort food
5 from 1 vote
Print Pin Rate
Course: Main Course
Cuisine: American
Keyword: spaghetti squash recipe
Prep Time: 15 minutes
Cook Time: 40 minutes
Total Time: 55 minutes
Servings: 4 Servings
Calories: 137kcal
Author: Angela Coleby


  • 1 Spaghetti Squash
  • 2 Chipolte peppers from tin chopped and with sauce
  • 2 ounces cream cheese
  • 1/2 cup Parmesan cheese grated
  • 1 teaspoon garlic powder
  • 1 teaspoon salt
  • 1 teaspoon black pepper


  • Cut the spaghetti squash in half length-ways and scoop out the seeds
  • Place the spaghetti halves cut side down on a plate in the microwave and cook for 15 minutes.
  • With a fork, scrape out the spaghetti strands and place in a bowl.
  • Add the chopped chipotle peppers, the sauce, cream cheese, garlic powder and Parmesan cheese.
  • Mix well and season with the salt and pepper.
  • Spoon the mixture into the spaghetti squash shells and spread evenly.
  • Bake at 200C/400F degrees for 20-25 minutes.
  • Serve as a main or side dish.


The net carbs will be the total carb count minus the fibre count. Carb count excludes sugar alcohols.
Any nutritional analysis on the website is based on an estimate, calculated by from the individual ingredients in each recipe. Variations may occur for various reasons, including product availability and food preparation. We make no representation or warranty of the accuracy of this information.


Serving: 1serving | Calories: 137kcal | Carbohydrates: 10g | Protein: 7g | Fat: 8g | Fiber: 1g
Tried this recipe?Mention @Divalicious_Recipes or tag #divaliciousrecipes

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  • Reply
    October 11, 2019 at 1:58 pm

    do you think this could be frozen and then thawed and cooked? I like spaghetti squash with Alfredo sauce but just being a 2 person household….it makes a lot. So i thought if I made both and halved each, it would at least taste different.

    • Reply
      Angela Coleby
      October 12, 2019 at 2:33 pm

      I haven’t tried to freeze it but can’t see why not. It is a very hearty dish and could keep you going for days!

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