
This post may contain affiliate links. Please read my disclosure policy.

About This Recipe
Growing up, I always loved spaghetti night! There was something just so comforting about a big bowl of spaghetti mixed with tender meat sauce and topped with melty cheese.
I knew when I started cooking healthier meals, I wanted to find a way to recreate this meal with a little less carbs and higher protein and this Spaghetti Squash Casserole is perfect for that!
This low carb, high protein Baked Spaghetti Squash Casserole is the perfect way to enjoy all the comforting, cozy tastes of traditional spaghetti without all the extra calories.
This dish is super simple to prepare and uses spaghetti squash noodles instead of traditional pasta to bring down the carbs. It also has double the protein of traditional pasta by making a creamy, high protein sauce with marina and cottage cheese! Trust me, it’s delicious!
And the best part about this dish is how great it is for meal prep and reheating throughout the week! Just like traditional pasta, this spaghetti squash casserole is perfect for prepping in advance and enjoying for a quick lunch or easy weeknight dinner throughout the whole week!
If you like a bit of heat, check out my Buffalo Chicken Spaghetti Squash Casserole! You may also enjoy my Cheesy Spinach and Artichoke Spaghetti Squash Bake or my Cheeseburger Spaghetti Squash Casserole!

Why You’ll Love This Baked Spaghetti Squash Casserole
- Only 7 simple ingredients! With one being a seasoning. That is it!
- Packs MAJOR VOLUME and super filling! One serving size is 1/8 of the dish!
- Healthy but indulgent! This dish is packed with quality protein and vegetables!
- Super maco-balanced! Only 220 calories and 15g of carbs for one huge serving!
- Great for meal prep – make once and you have dinner for the week!

- Spaghetti squash – I used a large spaghetti squash and got about 5-6 cups (750g) from it once baked. Check out these 3 easy ways to cook spaghetti squash!
- Lean ground beef – I used 96% lean ground beef to keep this dish lighter in fat, but feel free to use a different beef or even ground chicken or turkey!
- Cream cheese – I used fat-free to keep this dish lighter. But if you can’t find fat-free or just want to use something else, 1/3 reduced fat or full-fat cream cheese would work.
- Cottage cheese
- Marinara sauce – I love Rao’s but any marinara sauce will work!
- Tony’s creole seasoning – Any type of seasoning works for this recipe!
To make dairy-free: use dairy-free cream cheese and sub cottage cheese for extra dairy-free cream cheese or dairy-free Greek yogurt.
- Use ground turkey or ground chicken instead of ground beef!
- Trade the marinara sauce for a yummy alfredo!
- Add extra veggies! Throw in some mushrooms, bell peppers, onions, tomatoes or spinach!
- Make vegetarian by subbing with your favorite plant-based meat alternative.
How To Make
The full printable recipe is below, but let me walk you through the process so you know what to expect when you’re making it!

1. Cook spaghetti squash. Preheat the oven to 400F. Cut spaghetti squash in half lengthwise, then scoop out the seeds from the center of both halves. Place halves of squash flesh side down in a 9×13 pan sprayed with cooking spray. Bake for 30-40 minutes, or until tender. Let cool, then use a fork to pull out strands of the flesh.

2. Bring a skillet to medium heat. Add the beef and season with 1 tsp of creole seasoning and salt and pepper to taste. Crumble the beef as it cooks. Once beef has cooked through, turn off heat and set aside.

3. In a large mixing bowl, add softened cream cheese, cottage cheese, and 1 Tbsp of creole seasoning. Using a hand mixer, blend until everything is combined.

4. Add the marinara sauce and stir until it has mixed in thoroughly.

5. Then, add in the beef and spaghetti squash strands (make sure you drain the water from them first!) to your dish.

6. Top with the marinara and cheese mixture.

7. Sprinkle with cheese and bake for about 30 minutes, or until hot and bubbly.

8. Serve and enjoy!
Helpful Tips
This baked spaghetti squash casserole truly is so easy! The hardest part is just getting your spaghetti squash cooked and shredded – besides that, everything else comes together relatively quick and easy.
If you aren’t sure the best way to cook your spaghetti squash, check out these 3 easy ways (oven, air fryer, microwave) to bake and shred your squash. I will usually do this the night before so I have the strands ready to go.
Just like any other casserole, I would throw alongside some sides that sound good with it! Here are some of my favorite things I have enjoyed eating this baked spaghetti squash casserole with:
- Seasoned green beans or broccoli.
- Upside Down Egg White Pizza – YOU MUST TRY IT!
- Garlic bread, garlic knots, or rolls!
- Side romaine salad with pickled red onions.
- Spinach salad with feta.

What is the best way to cook spaghetti squash?
There are several easy ways to cook spaghetti squash. You can bake it in the oven, cook in the microwave or air fry it. I personally love roasting it in the oven (if I have time) because I think it brings about the best flavor but truly any work! I also like to cook and shred my squash the night before if I have time to make this casserole prep even easier!
Can I freeze this spaghetti squash casserole?
Yes! This is a great casserole to freeze. Just let it come to room temperature, then store it covered or in a plastic container for up to 3 months. To reheat, let it defrost in the fridge overnight then reheat in the oven at 350F for 20-30 minutes, or until the center is warm and the casserole is bubbling again.
Why is my spaghetti squash casserole watery?
Be sure to not overcook your spaghetti squash as this can cause it to be watery and add too much liquid to the dish. I like to bake my spaghetti squash until it is just barely done (able to shred with a fork) because it will continue to cook in the oven with the dish. This prevents overcooking and the casserole turning out watery.
Did you make this? If you snap a photo, please be sure leave a review, tag me on Instagram or TikTok at @LaurenFitFoodie or hashtag #LaurenFitFoodie so I can see your creations!

Baked Spaghetti Squash Casserole (Low Carb, High Protein)
Ingredients
- 1 lb. 96% lean ground beef
- 5-6 cups spaghetti squash (750g) shredded, drained of water, and loosely packed
- 1 tbsp + 1 tsp Tony’s Creole seasoning separated
- 8- oz. reduced-fat cream cheese (224g) softened
- 1/2 cup low-fat 2% cottage cheese (117g)
- 1 24-oz. jar marinara sauce I love Rao’s
- 3/4 cup shredded whole milk mozzarella cheese (84g)
Before You Begin! If you make this, please leave a review and rating letting us know how you liked this recipe! This helps our business thrive & continue providing free recipes. Scroll for macros and MyFitnessPal code.
Instructions
- Cook spaghetti squash. Preheat the oven to 400 degrees Fahrenheit. Cut spaghetti squash in half lengthwise, then scoop out the seeds from the center of both halves. Place halves of squash flesh side down in a 9×13 pan sprayed with cooking spray. Bake for 30-40 minutes, or until tender. Let cool, then use a fork to pull out strands of the flesh.
- Preheat the oven to 350 °F. Spray a 9×13" dish with cooking spray and set aside.
- Bring a skillet to medium heat. Add the beef and season with 1 tsp of creole seasoning and salt and pepper to taste. Crumble the beef as it cooks. Once beef has cooked through, turn off heat and set aside.
- In a large mixing bowl, add softened cream cheese, cottage cheese, and 1 Tbsp of creole seasoning. Using a hand mixer, blend until everything is combined.
- Add the marinara sauce and stir until it has mixed in thoroughly.
- Then, add in the beef and spaghetti squash strands (make sure you drain the water from them first!) and fold in until all ingredients are combined.
- Add the spaghetti squash mixture to the baking dish and spread out evenly. Sprinkle with cheese and bake for about 30 minutes, or until hot and bubbly.
Equipment
Notes
Nutrition Information
Nutrition is hand-calculated and accurate. No autocalulations! However, note that values can vary based on the brands you use and if you substitute ingredients.