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Cook up a dreamy, cheesy meal with this Broccoli Cheddar Spaghetti Squash Casserole. It’s like your favorite soup transformed into a casserole and combined with other flavor-bomb ingredients!

A deliciously cheesy broccoli cheddar chicken casserole
Broccoli cheddar lovers, listen up! Today we’re giving the classic flavor combo a spin and baking it casserole-style with this delicious broccoli cheddar spaghetti squash casserole creation.
The dish features the obvious: cheddar cheese and broccoli, but it also includes flavorful ingredients like minced garlic, onion, spaghetti squash, and even Greek yogurt. It’s a multi-layered dish that you’re going to devour!
If you’ve never cooked with spaghetti squash, don’t worry. This detailed tutorial will walk you through it! It’s a great ingredient to add to meals for filling them with low-calorie density and great taste.

Ingredients in baked spaghetti squash casserole
- Spaghetti squash: Start with 1 whole spaghetti squash. It should be around 2-2.5 lb and amount to 4 cups after being cooked and shredded.
- Chicken: Next, you will need 4 cups of cooked chicken. You can bake and dice it or use pulled chicken from a rotisserie.
- Avocado oil: Use 2 tbsp of avocado oil to cook the onion and broccoli.
- Onion: As for the onion, you’ll need 1/2 of a large yellow onion, diced.
- Broccoli: Next, roughly chop up 5 cups of broccoli.
- Garlic: Add flavor with 4 cloves of minced garlic.
- Yogurt: 1 cup of plain Greek yogurt will be used to add consistency and flavor to the casserole.
- Cheese: Add delicious cheesiness with 1.5 cups of cheddar, divided.
- Seasonings: Add additional flavor by including 2 tsp of salt, 1/2 tsp of pepper, 2 tsp of garlic powder, and 2 tsp of onion powder.
- Eggs: Finally, you will need 2 whisked eggs.
Tools needed to create this recipe
To make broccoli cheddar spaghetti squash casserole, you will need a baking dish and nonstick spray. You’ll also need a large pan, spatula, large mixing bowl, stirring utensil, and whisk.
For measuring, grab the following sized cups: 1/2 tsp, 1 tsp, 1 tbsp, 1/2 cup, and 1 cup.


How to make broccoli cheddar spaghetti squash casserole
You’re just over an hour away from an ooey, gooey, cheesy, and warm casserole that tastes delicious and is so satisfying! You will need about 10 minutes for prepping and around an hour for cooking and baking.
First, preheat the oven to 400°F and grease a 9×13 baking dish.
Prepare the spaghetti squash according to this recipe, or use your preferred squash cooking method.
Then, prepare the chicken. I used a rotisserie and it worked great!
Heat the avocado oil in a large pan over medium-high heat and add the onion. After one minute, add the broccoli.
Cook the onions and broccoli for 6-7 minutes or until they begin to tenderize, and then add the garlic for the last minute of cooking. Turn off the heat.
In a large bowl, add the spaghetti squash, chicken, broccoli and onions, Greek yogurt, 1 cup of cheese, salt, pepper, garlic powder, and onion powder. Stir until well combined.
Add the whisked eggs. Stir until everything is mixed well.
Pour the mix into the greased baking dishes and top with the remaining cheese.
Bake for 45-50 minutes, or until the inside is set and bubbling.
Let cool for 15 minutes before eating.

Substitution Tip
Throughout this recipe there are a couple of substitutions you can try out.
Avocado Oil
You can use any cooking oil — olive, coconut, canola, vegetable, etc. If using coconut, choose a refined version so you don’t wind up with a coconut flavor.
Yellow Onion
Though I recommend yellow onion in this dish, white or red will also work!
Cauliflower
Feel free to switch the broccoli for cauliflower if that’s more your style.
Cheddar Cheese
Cheddar can be replaced with your favorite cheeses like pepper jack, mozzarella, or even Swiss!
If you liked this recipe, you’ll want to try these!
I love combining squash into my casseroles and even using it in soup! Here are some yummy squash recipes using both spaghetti and butternut variations.
- Lemon Chicken Spaghetti Squash Casserole
- Butternut Squash Soup (Vegan, Dairy-free)
- Barbecue Chicken Spaghetti Squash Boats
Recipe by Erin Antoniak and Photos by Bake and Bacon

Broccoli Cheddar Spaghetti Squash Casserole
Cook up a dreamy, cheesy meal with this Broccoli Cheddar Spaghetti Squash Casserole. It’s like your favorite soup transformed into a casserole and combined with other flavor-bomb ingredients!
Ingredients
- 1 spaghetti squash (2 – 2.5 lb, cooked and shredded) – about 4 cups
- 4 cups cooked chicken, diced or pulled rotisserie
- 2 tbsp avocado oil
- 1/2 large yellow onion, diced
- 5 cups roughly chopped broccoli
- 4 cloves garlic, minced
- 1 cup plain Greek yogurt
- 1.5 cups cheddar cheese (divided)
- 2 tsp salt
- 1/2 tsp pepper
- 2 tsp garlic powder
- 2 tsp onion powder
- 2 eggs, whisked.
Instructions
- Preheat oven to 400F and grease 9×13 baking dish.
- Prepare your spaghetti squash according to this recipe, or however else you make cooked spaghetti squash. Prepare your chicken as well. I used rotisserie chicken for this and it worked great.
- In a large pan, heat avocado oil and onion over medium-high heat. After a minute, add in broccoli.
- Cook onions and broccoli for 6-7 minutes or until begin to tenderize, and then add garlic for last minute of cooking. Turn off heat.
- In a large bowl, add spaghetti squash, chicken, broccoli and onions, greek yogurt, 1 cup of cheese, salt, pepper, garlic powder, and onion powder. Stir until well combined.
- Add in whisked eggs and stir until everything is mixed together well.
- Pour into greased 9×13 baking dish. Top with remaining cheese.
- Bake for 45-50 minutes or until inside is set and bubbling.
- Let cool 15 minutes before eating.
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Emma D says
This was so good!! I feel like I haven’t had something like this before so it was nice to switch it up for meal prep. It was extra cheddar-y which I loved.
Erin says
Hi Emma, so glad you loved it!!
Maddy says
Yo favorite go to recipe!
Katie says
Made last night per instructions. Added in some mushrooms just for a little more vegetables and thought I would also like the added taste. I thought it was great! I’m needing it throughout the week for my lunches at work/school. Love all the spaghetti squash casserole recipes! Thank you!
Erin says
Hi Katie, so happy you loved it and made it your own!! 🙂