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Overhead shot of chili spaghetti squash casserole in a large casserole dish. It is topped with sliced avocado and cilantro. Next to it is a bowl of corn chips, bowl of cilantro, and half an avocado.
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4.7 from 10 votes

Chili Spaghetti Squash Casserole

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!
Course Main Course
Cuisine American
Keyword baked spaghetti squash casserole, chili casserole, Spaghetti Squash Casserole, spaghetti squash casserole with ground beef
Prep Time 5 minutes
Cook Time 1 hour
Resting Time 5 minutes
Total Time 1 hour 10 minutes
Servings 8
Calories 344kcal
Author Kelly


  • 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...


  • 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!


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.


Serving: 1piece | Calories: 344kcal | Carbohydrates: 23g | Protein: 31.6g | Fat: 14.2g | Saturated Fat: 5.9g | Polyunsaturated Fat: 1.2g | Monounsaturated Fat: 5.2g | Potassium: 914mg | Fiber: 6.4g | Sugar: 8g | Vitamin A: 2317IU | Vitamin C: 86mg | Calcium: 162mg | Iron: 4.5mg