All of your favorite chili ingredients combined into one delicious and comforting baked spaghetti squash casserole with ground beef. This healthy casserole recipe is great for a satisfying meal, meal prep, and is also gluten-free and low-carb!

It’s chili season! And casserole season! And we are giving you the best of both worlds today with this chili spaghetti squash casserole.

It takes all your favorite chili ingredients – ground beef, peppers, onions, beans, fire-roasted tomatoes, warming spices, and cheese – and packs it into one hearty and comforting meal.

We love this casserole because:

• it’s made from simple ingredients
• it’s packed with protein and veggies
• makes a decent amount so we always have leftovers and/or is great for meal prep!
• it’s the best of both worlds – chili and casserole!

How to cook spaghetti squash

There are a few ways to bake spaghetti squash depending on the time you have the kitchen appliances you have. Here are my top ways:

1. Oven-baked spaghetti squash – preheat oven to 375 degrees and cut the squash in half length or width-wise. Lengthwise is more common, but if you cut it width-wise, you will get longer strains of spaghetti (good if you are using it as spaghetti). Rub a little oil and salt and pepper on the flesh and place face down on a lined baking sheet. Roast for 40-45 minutes until the skin gives and can easily be threaded.
2. Instant Pot spaghetti squash – add about 1-2 cups of water to your Instant Pot with the steamer insert. Cut in half width-wise, place squash in your Instant Pot, and cook on high pressure for 10 minutes. I’ve also heard you can cook it without cutting it in half, but I haven’t tried it that way.
3. microwave spaghetti squash – I haven’t tried this, but you can check out this post. All you need to do is cut it in half, place flesh side down in a glass baking dish, fill that dish with about an inch of water, and microwave for 10 minutes until cooked.

How to make chili spaghetti squash casserole with ground beef

This healthy spaghetti squash casserole makes a well-balanced meal with protein, healthy fats, and veggies. By using spaghetti squash, it is low carb and keto friendly. If you bake the spaghetti squash ahead of time, it saves a bunch of time and makes an easy weeknight dinner. And it’s perfect for meal prep!

Chili spaghetti squash casserole ingredients:

• spaghetti squash
• oil
• ground beef – I suggest 93/7 or leaner
• onion
• bell peppers
• chili powder
• cumin
• paprika
• red pepper flakes
• black beans
• fire-roasted tomatoes
• eggs
• cheddar cheese
• salt and pepper

First, start off by cooking your spaghetti squash. I cooked mine in the Instant Pot, but you can cook it according to one of the other ways above.

When you have about 15 minutes left on the spaghetti squash, start to make the beef and veggie mixture. Heat up a large cast-iron or skillet and add oil. Add the onions and some salt and pepper and saute for 3-4 minutes.

Then add the beef and saute for 4-5 more minutes until mostly browned. Next, add the peppers and saute for another 3-4 more minutes until softened. Stir in the spices.

When the spaghetti squash is done, add it to a large greased baking dish (I used a 13×9). Next, add the beef mixture along with your black beans, tomatoes, and eggs. Mix well to combine and evenly distribute all the ingredients. If it is easier, you can mix everything up in a bowl, but I like to save an extra dish to wash.

Then sprinkle with your cheddar cheese. Finally, bake at 375 for 40-45 minutes until the mixture is set and is crispy around the edges. Let cool for 3-4 minutes and enjoy!

I like topping mine with a little cilantro, hot sauce, avocado, and sour cream or greek yogurt.

How do you keep squash casserole from getting watery?

A few factors play into how this casserole will turn out. Due to the nature of the ground beef and spaghetti squash, will have a little excess liquid, but don’t want too much.

1. First, make sure you are using lean ground beef (I recommend 93/7 or leaner). When transferring the cooked mixture to your casserole, make sure to leave all the fat/liquid behind.
2. Second, don’t overcook your spaghetti squash. If it overcooks, it gets watery/mushy. If needed, you could put it in a colander and let sit to drain any excess liquid.

Is spaghetti squash low in carbohydrates?

Yes, spaghetti squash is a great low-carb alternative to pasta. It is packed with vitamins, minerals, and fiber with one cup (155 grams) only having 42 calories and 10 grams of carbs. On the other hand, pasta has 221 calories and 43 grams per one cup (140 grams).

Does spaghetti squash actually taste like spaghetti?

While spaghetti squash is a great substitute for pasta, it doesn’t taste like spaghetti. It has a slight nuttiness and sweetness to it, but is pretty mild and can go with so many flavors, making it a great healthy substitute for spaghetti.

Meal prep spaghetti squash casserole

Baked spaghetti squash casserole is a great dish to prep ahead of time or meal prep for the week! There are a few different ways you can meal prep it:

• Partial prep option #1 – make the spaghetti squash ahead of time and store it in the fridge. On the day of, make the beef and veggie mixture and mix with the already cooked spaghetti squash and remaining ingredients and bake.
• Partial prep option #2 – make the spaghetti squash and the beef and veggie mixture and store them separately in the fridge. Then, when you are ready to assemble, just put it in a large baking dish with the eggs, black beans, and crushed tomatoes, mix, top with cheese, and bake.
• Full prep – bake it and store it in the fridge for a quick meal during the week. Either reheat it in the oven or microwave depending on your setting.
• Freeze – if you want to freeze it, make it according to the directions and let cool completely. You can either freeze the whole dish or cut it into individual pieces and freeze it separately. When ready to eat, let defrost in the fridge or on the counter. Either bake it to warm through (if whole) or if you have an individual piece, bake it or microwave it.

If you have leftovers, just store them in the fridge in a tightly sealed glass container. You can also wrap your casserole dish with saran wrap. It saves well and should be good for up to a week.

Substitutions for chili casserole

This chili casserole recipe is super customizable. Here are some substitutions you could try:

• beef – you can use any kind of ground meat you like. Chicken and turkey would work great.
• beans – pinto or kidney beans would work the same in this recipe.
• fire-roasted tomatoes – if you don’t have canned fire-roasted tomatoes, you can use regular canned diced tomatoes.
• eggs – you can use egg whites instead of eggs, which will add a little more protein and lower the fat. If you can’t have eggs, you can leave them out and it will still work, they just help bind the casserole a little better.
• cheese – Monterey jack or pepper jack cheese would work instead of cheddar. You can also use dairy-free cheese or you can leave it off.

More healthy casserole recipes

• Beef Taco Casserole
• Buffalo Chicken Casserole
• Jalapeno Popper Chicken Casserole
• Ground Turkey Spaghetti Squash Casserole
• Chicken Fajita Casserole

4.70 from 13 votes

Chili Spaghetti Squash Casserole

Author: Kelly

All of your favorite chili ingredients combined into one delicious and comforting baked spaghetti squash casserole with ground beef. This healthy casserole recipe is great for a satisfying meal, meal prep, and is also gluten-free and low-carb!

Print Recipe

Course: Main Course

Calories: 344kcal

Protein: 31.6g

Carbs: 23g

Fat: 14.2g

Prep Time: 5 minutes

Total Time: 1 hour 10 minutes

Servings: 8

ingredients

• 1 medium-large spaghetti squash (about 1050 grams or 6.75 cups cooked spaghetti squash)
• 1/2 tablespoon oil
• 1 cup diced onion (120 grams)
• 2 pounds lean ground beef (I suggest 93/7 or leaner)
• 2 large bell peppers, diced (500 grams/4 cups)
• 1 tablespoon chili powder
• 1 tablespoon cumin
• 2 teaspoons paprika
• 1/2 teaspoon red pepper flakes
• 1 can (14.5 ounces) fire-roasted tomatoes, liquid slightly drained
• 1 can (15.5 ounces) black beans, rinsed and drained
• 2 large eggs, whisked
• 1 cup shredded cheddar cheese (3 ounces)
• optional toppings: cilantro, avocado, greek yogurt, sour cream, hot sauce...

instructions

• Preheat oven to 375 degrees Fahrenheit and grease a large casserole/baking dish (it need to be really large - I used a 13x9).
• Cook your spaghetti squash by your preferred method (oven, instant pot, or microwave). See notes below for each method.
• When you have about 15 minutes left on the spaghetti squash, start to make the beef and veggie mixture. Heat up a large cast-iron or skillet and add oil. Add the onions and some salt and pepper and saute for 3-4 minutes.
• Add the beef and saute for 4-5 more minutes until mostly browned. Next all the peppers and saute for another 3-4 more minutes until softened. Stir in the spices.
• When the spaghetti squash is done, add it to your greased 13x9 baking dish. Next, add the beef mixture, making sure to leave behind the grease (as much as possible), along with your black beans, tomatoes, and eggs. Mix well to combine and evenly distribute all the ingredients. If it is easier, you can mix everything up in a bowl, but I like to save an extra dish to wash. Top with cheddar cheese.
• Bake for 40-45 minutes until the mixture is set and is crispy around the edges. Let cool for 3-4 minutes to set. Cut into 8 equal-sized pieces, top with optional toppings, and enjoy!

notes

How to cook spaghetti squash:

1. Oven-baked spaghetti squash - preheat oven to 375 degrees and cut the squash in half length or width-wise. Lengthwise is more common, but if you cut it width-wise, you will get longer strains of spaghetti (good if you are using it as spaghetti). Rub a little oil and salt and pepper on the flesh and place face down on a lined baking sheet. Roast for 40-45 minutes until the skin gives and can easily be threaded.
2. Instant Pot spaghetti squash - add about 1-2 cups of water to your Instant Pot with the steamer insert. Cut in half width-wise, place squash in your Instant Pot, and cook on high pressure for 10 minutes. I've also heard you can cook it without cutting it in half, but I haven't tried it that way.
3. microwave spaghetti squash - I haven't tried this, but you can check out this post. All you need to do is cut it in half, place flesh side down in a glass baking dish, fill that dish with about an inch of water, and microwave for 10 minutes until cooked.

nutrition

Nutrition Facts

Chili Spaghetti Squash Casserole

Amount Per Serving (1 piece)

Calories 344 Calories from Fat 128

% Daily Value*

Fat 14.2g22%

Saturated Fat 5.9g37%

Polyunsaturated Fat 1.2g

Monounsaturated Fat 5.2g

Potassium 914mg26%

Carbohydrates 23g8%

Fiber 6.4g27%

Sugar 8g9%

Protein 31.6g63%

Vitamin A 2317IU46%

Vitamin C 86mg104%

Calcium 162mg16%

Iron 4.5mg25%

* Percent Daily Values are based on a 2000 calorie diet.

Tried this recipe?If you make this recipe or anything from Eat the Gains, leave a comment and rating to let people know how you liked it! Also, make sure to post it and tag me so I can see all of your creations!! @eatthegains and #eatthegains on Instagram!

This post may contain affiliate links and I may make a little bit of money if you click on and purchase the products through the links. It doesn’t cost you any extra money. The compensation helps with expenses to keep ETG up and running. I truly appreciate your support!