Low Carb Pesto Chicken & Spaghetti Squash Bake

This Low Carb Pesto Chicken and Spaghetti Squash Casserole is topped with mozzarella and tomatoes and SO unbelievably delicious! A one-dish Gluten Free, Keto Friend, and Kid-Friendly easy weeknight dinner!

A spatula removing one slice of the Pesto Chicken and Spaghetti Squash Casserole.
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Recipe Highlights

Before we get too far, let me tell you why this Low Carb Pesto Chicken recipe is the kind of dinner I love to make for my family.

  • First, it’s made in ONE dish, holla!
  • It can be prepped ahead of time, another score.
  • And you know what else? It’s sooooo unbelievably simple (It was on the table in under 20 minutes using prepped ingredients I already had).

Oh, and one other things: When I find a recipe my kids absolutely LOVE, I stick with it.

Because this recipe is made with 100% whole, clean ingredients (like my dairy-free pesto recipe), so it’s gluten free and low carb/keto friendly, but you’d never know it.

I’m convinced — This Low Carb Pesto Chicken & Spaghetti Squash is the casserole to beat all casseroles!

I call this recipe a Pesto Chicken UN-Casserole

When I think of casseroles, I think of canned creamy soup. Maybe with some kind of pasta? Definitely light on the veggies, too heavy on the cheese, and a generally delicious albeit not super healthy family-friendly dinner.

But this? This is the opposite of that. So this is a pesto chicken casserole… except it’s not.

Because it’s got a TON of veggies, lean protein, good fats, and just enough cheese to make it feel like a special dinner. So it’s an un-casserole.

Instant Pot Spaghetti Squash

Spaghetti Squash, a Magical Vegetable

You just need to awaken the magic of spaghetti squash with this pesto chicken, because it’s bursting with flavor! That kind of sounds like it should be the title of an old timey musical, no?

My favorite way to cook spaghetti squash:

  • In the Instant Pot! I poke a few 1/2 inch holes with a paring knife in the whole squash, then set it on the rack inside the IP. Add a cup of water to the bottom, set it to high for 7 minutes with a natural release. I allow it to cool, then scrape the seeds out quickly with a grapefruit spoon. Easy peasy!

I’m not saying spaghetti squash it’s exactly the same as real spaghetti, but it’s a pretty fantastic way to get your fix for something spaghetti-like while not actually eating pasta.

Whether you’re living a low carb, gluten free, or Whole30 lifestyle, spaghetti squash is an awesome addition to your weekly lineup. It’s almost like a blank canvas that nature made to look like spaghetti and trick our brains a little.

A collage of prep shots. On the left, a bowl with chicken, spaghetti squash, and pesto. On the right, it's all mixed together and in the casserole dish.
You can prep this meal ahead of time, then bake it just before you’re ready to serve it! It fed my family of 5 for 2 nights!

Now it definitely doesn’t taste like spaghetti. The flavor is super mild on its own. But I actually think that’s a big part of what makes it so awesome! Spaghetti squash totally holds up and works as the perfect vessel for hearty or meaty sauces.

Coming Soon: MORE Low Carb Recipes!

Do you eat Low Carb or Keto? Lately, I’ve had a lot of requests for Keto and Low Carb recipes on my site, and I had that in mind when I was making this pesto chicken casserole recipe. I’ve been excited to start experimenting with it more (I even put together a list of my favorite Keto and Low Carb Meatballs recipes!)

Keto recipes are absolutely #trending these days, but I’m mostly excited because I’ve heard from just as many people out there who’ve seen positive, healthy results by following a low carb meal plan, as from people who enjoy the recipes as part of their post-Whole30 Food Freedom.

Low Carb Pesto Chicken and Spaghetti Squash Casserole, close up shot of finished dish.

Here’s what I’m going to do: Keep focusing on creating recipes that are made with whole, nutrient dense foods, because that’s just my style.

A hand pulls a piece of chicken and melty cheese from a the casserole.

Looking for more? Just check out some of these delicious recipes:

I hope you love this Low Carb Pesto Chicken and Spaghetti Squash Casserole recipe, topped with mozzarella and tomatoes. It’s one of my favorite family-friendly meals of all time!

Pin it for later:

Low Carb Pesto Chicken and Spaghetti Squash Casserole, finished dish with words, "Chicken and Pesto Spaghetti Squash Casserole" Pinterest Image

Will you make this recipe? I’d LOVE to see it! Please tag me on Instagram @cookathomemom!

5 from 10 votes

Pesto Chicken and Spaghetti Squash Bake (Low Carb, Gluten Free)

Low Carb, Gluten Free, Family Friendly

Course Dinner
Cuisine American, Italian
Keyword Family Friendly, One Pan Meal
Prep Time 10 minutes
Cook Time 15 minutes
Total Time 25 minutes
Servings 4 servings
Calories 948 kcal


  • 5 cups cooked spaghetti squash about 1 small-medium squash
  • 2 1/2 cups chicken breasts about 1 lb, cooked
  • 1 cup pesto
  • salt and pepper to taste
  • 1/2 tsp garlic powder
  • 1/2 tsp onion powder
  • 8 oz grated mozzarella cheese about 1 1/2 cups
  • 3 tbsp parmesan cheese
  • 2-3 medium tomatoes


  • 1 1/2 cups packed basil leaves
  • 1 clove garlic blanched
  • 1/4 cup pine nuts
  • 1/4 cup sunflower seeds
  • 3 tbsp lemon juice
  • 1/4 tsp salt
  • 1/4 tsp pepper
  • 1/4 cup parmesan reggiano cheese grated
  • 1/2 cup olive oil


Prepare Squash

  1. Cook the squash your preferred way – I cook it in the Instant Pot or roast it in the oven. Scoop the seeds out and scrape the squash out with forks, breaking it up a bit and fluffing it up as you remove it. 

Make the Pesto

  1. Add all the ingredients except the oil to your high speed blender or food processor. Pulse a few times until combined. 

  2. Add the oil and blend together on low until fully combined. Add additional oil if necessary until it reaches your desired consistency, 1 teaspoon at a time. 

Prepare the Dish

  1. Preheat your oven to 400 degrees. Chop or shred the chicken into bite-sized pieces. Slice the tomatoes into 1/2 inch slices and set them aside.

  2. In a large bowl, toss the chicken, spaghetti squash, pesto and seasonings together. 

  3. Pour the mixture into to a 10-inch casserole dish and gently press the mixture down. 

  4. Sprinkle the mozzarella and parmesan cheese over the spaghetti squash mixture, then lay the tomato slices on top. 

  5. Bake for 12-15 minutes, until the cheese is melted and it’s heated through. You can finish it under the broiler for a minute or two to brown the cheese a bit, if you’d like!

Nutrition Facts
Pesto Chicken and Spaghetti Squash Bake (Low Carb, Gluten Free)
Amount Per Serving
Calories 948 Calories from Fat 702
% Daily Value*
Fat 78g120%
Saturated Fat 18g113%
Cholesterol 117mg39%
Sodium 1370mg60%
Potassium 775mg22%
Carbohydrates 20g7%
Fiber 4g17%
Sugar 8g9%
Protein 44g88%
Vitamin A 2834IU57%
Vitamin C 18mg22%
Calcium 558mg56%
Iron 3mg17%
* Percent Daily Values are based on a 2000 calorie diet.

Roasted Spaghetti Squash cut in half and stuffed with meatballs, red marinara sauce, and topped with fresh basil.

Looking for more Spaghetti Squash awesomeness? Check out my recipe for Whole30 Spaghetti Squash & Meatball Marinara.