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Pesto Chicken Spaghetti Squash (Paleo + Whole30)

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Pesto Chicken Spaghetti Squash – This yummy pesto spaghetti squash bake packs a TON of flavor with only four main ingredients. A winner all around! (Gluten Free, Dairy Free, Paleo & Whole30 Approved!)

Close up of Pesto Chicken Spaghetti Squash (Gluten Free, Paleo & Whole30)

Happy New Year!!! I’ve been dying to post this recipe since I teased a few pictures of it on Instagram stories a few weeks ago, but promised that I’d take a few weeks off at the end of the year. (In 10+ years, I’ve never taken a break that long before, and it’s been wonderful/weird!).

But, friends, today is the day! This Pesto Chicken Spaghetti Squash is the kind of recipe I love. It’s an all-in-one, delicious healthy meal that’s PERFECT for getting back to your regular eating habits after enjoying all the holiday feasting. It’s PACKED with flavor, has only 4 main ingredients and looks gorgeous to boot! (Plus, it’s gluten free, paleo, and Whole30.)

Here’s why it’s so good even Sophie had seconds…

Pesto Chicken Spaghetti Squash Bake ready to go into the oven!

What Makes this Pesto Chicken Spaghetti Squash Amazing:

Big, bold flavors. First off, there’s the incredible combination of pesto + tomatoes, which gets me every time. I use my homemade dairy free pesto (it’s EASY and can even be nut free!)

This recipe is blessedly easy. With just 4 main ingredients, this is about as simple as it gets. Roast or cook your squash, then stir it up with some pesto and chicken. Put it in a baking dish, top with sliced tomatoes, and broil or bake to finish. Done!

It’s meal prep friendly. If you’re a meal prep fan, you can easily do a few steps ahead of time to make this dinner come together in a flash. For instance, you can save a bunch of time by roasting your squash ahead of time and using pre-cooked or leftover chicken (rotisserie, roasted, grilled, poached, whatever you like!).

You can make it Whole30 approved! My dairy free pesto (linked above and below) is gluten & dairy free, and totally Whole30 approved. You end up with a dish that feels beautifully satisfying without feeling like you’re “missing” anything.

Close up of Pesto Chicken Spaghetti Squash (Gluten Free, Paleo & Whole30)

How to Cook Your Spaghetti Squash:

There are LOTS of ways to cook spaghetti squash, but my number one pick is…

Roasting (My Favorite): Any time you have the time, I recommend roasting your spaghetti squash. I feel like the strands have the best texture (more of the liquid evaporates) and some of the natural sweetness of the squash develops. Plus, with the extra time, the flavor of the olive oil and the salt & pepper meld beautifully with the squash as its cooking. For flavor and texture, it scores highest on my list. (See the recipe card for my full roasting method)

The only downside of roasting (in my opinion) is that it *does* take 35-45 minutes to get your squash tender and develop some of that lovely caramelization around the edges. (You can save a bit of time with this shortcut method of roasting if you prefer.) I usually put it in the oven when I’m doing something else (folding laundry, making breakfast for the kids or cleaning up dinner, loading/unloading the dishwasher, helping to pack school lunches, etc.).

Or, if you’re in a hurry, you might want to go with one of these methods…

Instant Pot: Using the Instant pot or pressure cooker does cut down on the cook time, and definitely feels more hands off. For me, it doesn’t nail the same notes texturally or from a flavor standpoint. It can also tend to hold onto liquid as it cooks, which can mean extra water in your recipes (this = watered down recipes). (Here’s a tutorial for Instant Pot Spaghetti Squash + Slow Cooker directions)

Slow Cooker: Similar to the Instant Pot/pressure cooker method, using a slow cooker to cook spaghetti squash definitely removes any hands-on element. You truly get to set and forget it. The only downside for me is that you can run into the same excess liquid issue with the slow cooker that you can get with the pressure cooker. (The lid traps steam and prevents much evaporation, which can trap the water/steam in the squash.) It’s not a deal breaker, but can occasionally lead to watered down sauces or recipes.

Microwave: This method might be the fastest of all, but it scores pretty low for me texturally. It’s hard to nail that perfect “al dente” texture in the microwave, and requires regularly checking it. On the plus side, it is fast and easy. Here’s how to cook spaghetti squash in the microwave.

Bowl of Pesto Chicken Spaghetti Squash with tomatoes.

Extra Add-ins & Ideas for Changing it Up:

I love experimenting with recipes (see my 7 Ways With Overnight Oats or 6 Amazing Ways to Stuff a Baked Sweet Potato posts for evidence). That said, this base recipe is TERRIFIC. The pesto adds loads of flavor on its own, and with the chicken and tomatoes, it’s hearty and satisfying. But, if the mood strikes and you want to try playing with the recipe…

  • Try adding 3-4 slices of cooked, crumbled bacon. The smokiness and extra saltiness is really nice!
  • Use grilled chicken instead of poached/roasted/rotisserie.
  • Stir in 1/2 cup of roasted red bell pepper slices to the squash mixture. (Jarred are fine! Trader Joe’s and Jeff’s Naturals are both Whole30 approved, I believe)
  • Switch out the basil pesto for sun-dried tomato pesto or add a few sun dried tomatoes to the mixture. (Jeffs Naturals brand are Whole30 approved)
  • Add cheese (if you tolerated it). We’re dairy free these days, but I can guarantee that a generous handful of Parmigiano Reggiano would be dynamite on top before it goes into the oven. (Note: not Whole30 approved)
Close up of Oval baking dish of Pesto Chicken Spaghetti Squash (Gluten Free, Paleo & Whole30)

Notes on this Pesto Chicken Spaghetti Squash:

Not into spaghetti squash? I understand! It’s not everyone’s cup of tea. If you’re not following a grain free or Whole30 plan, you can absolutely swap in 10-12oz of cooked pasta (gluten free or traditional, as needed). Know that pasta tends to absorb some of the pesto, so you may want to add an extra 3-4 Tbsp of pesto to the recipe so it’s not dry.

Shortcut tips: To make this easy for a weeknight, consider roasting your squash ahead of time. It takes 35-45 minutes to roast (see my tips above for other methods), so I usually do that ahead of time so the squash is cooked and ready to go. Then, you can use pre-cooked chicken (this is a great time for leftover cooked chicken or a rotisserie chicken!).

Can I double this recipe? Yep! You can. Just put it in a 9×13″ baking dish instead of the 2-quart (or 8×8″) baking dish I use here. Cook time shouldn’t be much different–you’ll just add an extra minute or two.

Oval baking dish of Pesto Chicken Spaghetti Squash (Gluten Free, Paleo & Whole30)

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Close up of Pesto Chicken Spaghetti Squash (Gluten Free, Paleo & Whole30)

Pesto Chicken Spaghetti Squash (Paleo + Whole30)

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5 from 4 reviews

  • Author: Emily
  • Total Time: about 20 minutes (once squash is cooked)
  • Yield: 6 generous servings 1x


This yummy pesto spaghetti squash bake packs a TON of flavor with only four main ingredients. A winner all around! (Gluten Free, Dairy Free, Paleo & Whole30 Approved!)


  • 1 (2.5-3lb.) spaghetti squash (about 6 cups cooked squash)*
  • 1012oz. cooked, cubed or shredded chicken breast (about 2 cups)
  • 3/4 cup pesto, such as this dairy free pesto
  • 45 Roma tomatoes, sliced (enough slices to cover the top of your baking dish
  • salt and pepper, to taste
  • 23 tsp olive oil


Roast Your Squash* (See notes for alternative cooking methods)

  1. Preheat oven to 400 degrees F. Cut your squash lengthwise and remove the seeds with a spoon. Drizzle or brush with olive oil and sprinkle with salt and pepper.
  2. Place squash cut side down on a baking sheet and roast at 400 degrees 35-45 minutes, or until strands are tender and easily come away from the sides (I like to wait until the edges of the squash are just starting to caramelize where it touches the pan).
  3. Shred the strands of spaghetti squash away from the skin and discard skin. You should have about 6 cups shredded squash.

Prepare & Assemble Your Recipe:

  1. Set oven to broil setting to pre-heat.
  2. Add cooked spaghetti squash strands to a large bowl. Add chicken and pesto and stir to combine well.
  3. Transfer pesto squash mixture to a 2-quart (or 8×8″) baking dish and smooth out the surface, packing it down slightly.
  4. Top with sliced tomatoes. Sprinkle with salt and pepper. (Optional: you can brush the tomatoes with a tiny bit of olive oil or drizzle a little over the top if you like).
  5. Broil for 5-7 minutes, or until tomatoes are just starting to blister. (Check regularly to prevent burning). (Alternatively, you can bake the squash at 400 degrees for 20-25 minutes)
  • Prep Time: 15 minutes
  • Cook Time: 5 minutes
  • Category: Casserole, main dish, chicken
  • Method: bake, broil
  • Cuisine: American


  1. I know I am going to love this, as I have made something similar to this on my own (though with the use of a few pots and pans) 😁 I never tried cooking everything at once, though, so
    I am excited! Thank you 💕

  2. This is so delicious!! I cut the recipe in half and my boyfriend and I ate the entire thing with some baked French bread. He kept saying “This is one of the best things I’ve eaten in so long.” Thank you! I did a vegan pesto – basil, arugula, walnuts, garlic, nutritional yeast, olive oil, and lemon – it’s my go to. I think I used more than was suggested. I let the squash roast 45 minutes – it was perfect. And got to use a tomato fresh from the garden!! I added some freshly grated Parmesan to the top before putting it in the oven under broil. We let it broil for a long time – and near the end left the oven door open to help evaporate the moisture from the tomatoes. The tomatoes got black spots – little caramelized spots of goodness! The tomatoes really make this over-the-top! TOTAL KEEPER!

  3. This was delicious. It was easy to make. I think will be my go to recipe for spaghetti squash!
    Thank you, Emily.

  4. Thank you so much!! Wow! What a delicious, dairy-free, paleo recipe! I tried this out last week and my husband and I had to use lots of self restraint not to eat all of it in one sitting. Great combination of flavours! Thank you =) I was unable to get spaghetti squash due to it’s being out of season, so I used grated zucchini which I roasted in the oven.

  5. Could you cook the squash ahead of time? Or assemble this earlier in the day to be baked in the evening? I worry about more moisture from the squash being released, that’s what I’ve never liked about spaghetti squash…but we have two from our summer garden that need to be used up. But I don’t always have time to bake the squash, AND assemble, AND bake the finished product….

    1. Jennifer – Absolutely. I often cook the squash ahead of time and store it in the fridge till I’m ready to assemble the whole dish. No worries at all!

  6. Looks great! I can’t figure out what makes the fat % so high in the nutrition info. Can you help me figure that out? I try to stay about 6 grams/ serving, and from the ingredients, it seems like it would be fine, or even under. Thank you!

    1. Sue – The fat comes from the pesto (which is typically made from nuts or seeds and olive oil). I calculated the nutrition facts using my homemade pesto (which I recommend in the post), but you could certainly change the pesto if you’re looking to reduce the fat.

      1. Thanks! Should have recognized that… but I’m still kind of new at this analyzing thing. I think it’ll be on my cooking agenda this week or next!

  7. This looks delicious! Quick question…do you think I could add breadcrumbs on top of the tomatoes before broiling?

    1. That would probably be delicious! You may want to drizzle or mist the breadcrumbs with a little olive oil before broiling so they don’t scorch, then keep an eye on them since the broiler will brown them quickly.

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