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4.84 from 48 votes
Home By Course Main Entrees Dinner Casserole

Baked Spaghetti Squash Casserole (Low Carb, High Protein)

Baked Spaghetti Squash Casserole is an easy, low carb pasta-like dish that the whole family will love! Tender spaghetti squash strands combined with lean ground beef, marinara sauce and multiple cheeses to create a bubbly, cheesy marinara spaghetti bake! This dish is great for meal prep and can be enjoyed all week!

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By: Lauren published: Feb. 23, 2021 updated: Aug. 16, 2024 33 Comments

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Baked spaghetti squash casserole in a rectangle casserole dish.
Baked Spaghetti Squash Bake Pin.
Contents hide
About This Recipe
Why You’ll Love This Baked Spaghetti Squash Casserole
Ingredients and Substitutions
Optional Variations and Dietary Adaptions
How To Make
Helpful Tips
FAQ: Baked Spaghetti Squash Casserole
More Spaghetti Squash Recipes
Baked Spaghetti Squash Casserole (Low Carb, High Protein)
MyFitnessPal Entry
Did You Make This?

About This Recipe

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.

Growing up, I always loved spaghetti night! There was something just so comforting about a big bowl of spaghetti with 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 that was more macro-friendly and this Spaghetti Squash Casserole is perfect for that! 

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! Perfect for prepping in advance and enjoying for a quick lunch or easy weeknight dinner.

If you like a bit of heat, check out my buffalo chicken spaghetti squash casserole! You may also enjoy this spinach and artichoke spaghetti squash bake or this cheeseburger spaghetti squash casserole!

Zoomed in view of baked spaghetti squash casserole in a baking dish with a serving spoon after being baked.

Why You’ll Love This Baked Spaghetti Squash Casserole

  • Only 7 simple ingredients! With one being a seasoning. That’s it!
  • High volume dish (great if you’re working with lower calories)
  • Healthy but indulgent! Truly tastes like comfort food. 
  • Low in calories and carbs with moderate fat and protein.
  • Great for meal prep! Make once and have dinner for the week!

Ingredients and Substitutions

Ingredients for baked spaghetti squash casserole.
  • Spaghetti squash – I used a large spaghetti squash and got 5-6 cups (750g) after cooked. Check out these 3 easy ways to cook spaghetti squash!
  • Lean ground beef – I used 96% lean ground beef but use your preference, or even ground chicken or turkey!
  • Cream cheese – I used light cream cheese to keep this dish a little lower in fat. Any cream cheese works, even whipped cream cheese if you wanted.
  • Cottage cheese – it’s amazing in this! Greek yogurt or sour cream also work.
  • Marinara sauce – I love Rao’s because it is top notch quality marinara!  
  • Creole seasoning – this creole seasoning is so good with this recipe but can be subbed with any seasoning blend you had on hand, or make your own creole (see recipe card notes).

Optional Variations and Dietary Adaptions

To make dairy-free: use dairy-free cream cheese and sub cottage cheese for extra dairy-free cream cheese or dairy-free Greek yogurt.

  • Switch up the protein! Use ground turkey or ground chicken instead.
  • Alfredo! Trade the marinara sauce for a yummy alfredo.
  • Add extra veggies! Like mushrooms, bell peppers, onions, tomatoes or spinach.
  • Make vegetarian! Sub with your fav plant-based meat alternative or veggies.

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!

Cooked spaghetti squash in a baking dish.

1. Cook spaghetti squash first if you still need to. 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.

Ground beef cooking in a skillet.

2. Cook beef over medium heat. Season with 1/2 Tablespoon of creole seasoning and salt and pepper to taste. Crumble the beef as it cooks until no longer pink, then remove from heat.

Cream cheese, cottage cheese, and seasonings in a mixing bowl.

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

Marinara sauce in a bowl.

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

Cooked ground beef and spaghetti squash in a baking dish.

5. Add in the beef and spaghetti squash (make sure you drain the water from them first!) Or you can simply add directly to dish (like above).

Cooked ground beef and spaghetti squash covered in marinara sauce in a baking dish.

6. Top with the marinara and cheese mixture.

Spaghetti squash casserole topped with cheese in a baking dish before being baked.

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

Baked spaghetti squash casserole in a baking dish after being baked.

8. Serve and enjoy!

Prevent excess water!

Helpful Tips

It’s very important to not overcook your spaghetti squash here and to drain any excess water before mixing it with this recipe. Otherwise the dish will be more watery once you take it out of the oven.

It’s better to undercook it than overcook, as the squash will still cook some when it goes in the oven with this casserole. For more tips on how to cook a spaghetti squash, see this post.

Baked spaghetti squash casserole in a baking dish with a serving spoon after being baked.

FAQ: Baked Spaghetti Squash Casserole

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.

What to serve with this baked spaghetti squash casserole?

Any vegetable or side salad would be great! Some ideas: air fryer broccoli or green beans, honey butter yeast rolls, simple salad with goat cheese, or easy roasted cauliflower and carrots.

Why is my baked 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 (just able to shred with a fork) because it will cook more when we bake it in the casserole. This prevents overcooking and the casserole turning out watery.

More Spaghetti Squash Recipes

Buffalo chicken, spaghetti squash, and cheese baked in a casserole dish topped with green onions and dressing.

The BEST Healthy Buffalo Chicken Spaghetti Squash Casserole

Tuscan spaghetti squash in a baking dish.

Three-Cheese Tuscan Spaghetti Squash Bake (High Volume)

Cheeseburger spaghetti squash casserole in a baking dish with a wooden spoon.

Cheeseburger Spaghetti Squash Casserole (Low Carb + Low Calorie)

Spinach and artichoke spaghetti squash bake in a baking dish with a wooden spoon.

Cheesy Spinach and Artichoke Spaghetti Squash Bake (Low Carb)

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 in a rectangle casserole dish.
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4.84 from 48 votes

Baked Spaghetti Squash Casserole (Low Carb, High Protein)

? Gluten-Free ? High Protein ? Low Carb ? Macro-friendly
Baked Spaghetti Squash Casserole is an easy, low carb pasta-like dish that the whole family will love! Tender spaghetti squash strands combined with lean ground beef, marinara sauce and multiple cheeses to create a bubbly, cheesy marinara spaghetti bake! This dish is great for meal prep and can be enjoyed all week!
Yield: 8
Prep: 15 minutes mins
Cook: 30 minutes mins
Total: 45 minutes mins
Calories: 264kcal
Protein: 19.8g
Fat: 15.3g
Carbs: 11.8g

Ingredients

  • 1 lb. lean ground beef 96%
  • 5 cups cooked and shredded spaghetti squash (750g) loosely packed and DRAINED WELL!*
  • 1.5 Tbsp creole seasoning like Tony's, or homemade (see notes)
  • 8 oz. light cream cheese soft
  • 1/2 cup cottage cheese (112g)
  • 24 oz. marinara sauce Iike 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

  • Preheat the oven to 350 degrees F. Spray a 9×13-inch dish with cooking spray and set aside.
  • Cook beef over medium heat. Season with 1/2 Tablespoon of creole seasoning and salt and pepper to taste. Crumble the beef as it cooks until no longer pink, then remove from heat.
  • In a large mixing bowl, add softened cream cheese, cottage cheese, and the remaining 1 Tablespoon of creole seasoning. Using a hand mixer, blend until combined.
  • Add the marinara sauce and stir to combine.
  • Then, add in the beef and spaghetti squash (make sure you drain the water from them first!), fold to combine.
  • Transfer 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

  • Baking dish
  • Skillet

Notes

Homemade Creole seasoning:
  • 2.5 Tbsp paprika
  • 2 Tbsp salt
  • 2 Tbsp garlic powder
  • 1 Tbsp black pepper
  • 1 Tbsp onion powder
  • 1 Tbsp cayenne pepper
  • 1 Tbsp dried oregano
  • 1 Tbsp dried thyme
Mix the spices together and keep stored in an airtight container or jar. 
Spaghetti squash: make sure not to overcook your spaghetti squash (we want it al dente!) and to drain any excess water before mixing it with this recipe. Otherwise the dish will be more watery once you take it out of the oven. 
How to cook spaghetti squash: Preheat oven to 400 degrees F. 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.
See this post for three different ways to cook a spaghetti squash.

To make dairy-free: use dairy-free cream cheese and sub cottage cheese for extra dairy-free cream cheese or dairy-free Greek yogurt.
To make vegetarian: omit ground beef or sub with your favorite plant-based alternative or roasted veggies, like eggplant, bell peppers, onions, spinach, etc. 

Nutrition Information

Serving: 1/8 of dish (286g), Calories: 264kcal (13%), Carbohydrates: 11.8g (4%), Protein: 19.8g (40%), Fat: 15.3g (24%), Saturated Fat: 7g (44%), Fiber: 1.9g (8%), Sugar: 6.5g (7%)

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.

MyFitnessPal Entry

LFF Baked Spaghetti Squash Casserole

© Author: Lauren

Baked spaghetti squash casserole in a rectangle casserole dish.

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Lauren

Lauren lives with her husband, Simon and two dogs, Finley and Cookie, in the Carolina’s. She has college degrees in Nursing and Exercise Science, is a NASM certified trainer and spent many years as a macro coach before transitioning to full time blogging. She loves staying active, being creative and recreating her favorite comfort food dishes into healthier, lightened up versions. Desserts are her speciality!

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I’m Lauren, a food lover sharing healthy, macro-friendly recipes that taste good and you can feel good about eating. Here you’ll find everything from breakfasts to easy dinners to lightened up desserts because desserts are absolutely mandatory around here!

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