Low Carb Pesto Chicken & Spaghetti Squash Bake

5 from 14 votes

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!

Top down of a glass baking dish filled with the pesto chicken casserole, with one slice removed.

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.

Low Carb Pesto Chicken and Spaghetti Squash Casserole
  • 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
Low Carb Pesto Chicken ingredients in a bowl.
A Pesto Chicken Casserole with noodles and chicken, served low carb.

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 ways to cook spaghetti squash

  • Baked in the oven. Wash and cut the squash in half. Scoop out the seeds. Rub the flesh of each squash half with a little olive oil, salt, and pepper. Set face down on a parchment lined baking sheet. Bake at 400°F for 30-40 minutes or until soft.
  • Cooked 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 Pressure for 15 minutes, with a natural release. 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.

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.

Oh, and if you want to find great pesto, I recommend using my Dairy Free Pesto Recipe or getting Giovanni Rana brand in the refrigerated aisle. It’s delicious!

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!)

Low Carb Pesto Chicken and Spaghetti Squash Casserole

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.

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 person enjoying a bite of a Pesto Chicken Casserole.

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

Pin it for later:

Low Carb Pesto Chicken Casserole with spaghetti squash.

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!

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

Top down of a glass baking dish filled with the pesto chicken casserole, with one slice removed.

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

Low Carb, Gluten Free, Family Friendly
5 from 14 votes
Print Pin Rate
Prep Time: 10 minutes
Cook Time: 15 minutes
Total Time: 25 minutes
Servings: 4 servings

Ingredients

  • 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 teaspoons garlic powder
  • 1/2 teaspoons onion powder
  • 8 ounces grated mozzarella cheese about 1 1/2 cups
  • 3 Tablespoon parmesan cheese
  • 2-3 medium tomatoes

Pesto

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

Instructions

Prepare the Spaghetti Squash

  • Instant Pot Instructions: Poke a few small holes in the flesh of the squash. Add 1 cup of water to your Instant Pot. Set the squash on the trivet inside the pot. Cover and set to High pressure for 15 minutes, then allow for a NPR (Natural Pressure Release). Remove the squash, allow it to cool, then cut the squash in half. Scoop the seeds out and scrape the flesh of the squash out with forks, breaking it up a bit and fluffing it up as you remove it. 
    Oven Instructions: Wash and cut the squash in half. Scoop out the seeds. Rub the flesh of each squash half with a little olive oil, salt, and pepper. Set face down on a parchment lined baking sheet. Bake at 400°F for 30-40 minutes or until soft.

Make the Pesto

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

  • Preheat your oven to 400° F. Chop or shred the chicken into bite-sized pieces. Slice the tomatoes into 1/2 inch slices and set them aside.
  • In a large bowl, toss the chicken, spaghetti squash, pesto and seasonings together. 
  • Pour the mixture into to a 10-inch casserole dish and gently press the mixture down. 
  • Sprinkle the mozzarella and parmesan cheese over the spaghetti squash mixture, then lay the tomato slices on top. 
  • 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

Calories: 948kcal | Carbohydrates: 20g | Protein: 44g | Fat: 78g | Saturated Fat: 18g | Cholesterol: 117mg | Sodium: 1370mg | Potassium: 775mg | Fiber: 4g | Sugar: 8g | Vitamin A: 2834IU | Vitamin C: 18mg | Calcium: 558mg | Iron: 3mg
Did you try this recipe? Share it with us on Instagram! @cookathomemom!


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.

5 from 14 votes (7 ratings without comment)

Leave a Reply

Your email address will not be published. Required fields are marked *

Recipe Rating




16 Comments

  1. 5 stars
    I made this for dinner last Wednesday and it was delicious! I’m pretty sure it’s my new favorite way to eat spaghetti squash! This was amazing! My husband raved about and asked me to make it again two days later 🙂

  2. 5 stars
    I made this tonight and it was delish!!!! Thanks for the awesome and healthy inspiration!

    1. Hey Bella! Thanks for letting me know! I’m so happy you enjoyed it! 🙂 -Laura

  3. Do you cook the chicken first? I’m just not seeing it. Looking forward to making this! Thanks!

    1. Yes! It can be leftover grilled chicken, rotisserie chicken, whatever you have!

  4. 5 stars
    I love how you prep food. It is just one of the things I have learned from you. This is going on next week’s menu. I prefer the reds and orange for stuffing, and for some reason I like the horizontal cut. I think it is because of the proportion of filling to pepper. Anyway, thanks again. I really appreciate you.

  5. 5 stars
    I love trying new recipes with vegetables with my kids. My daughter is the master at the food processor and Kitchenaid mixer. We also love baking low carb desserts from your site!