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Make Spaghetti Squash Au Gratin in a casserole dish or muffin pan! Either way, this cheesy, low-carb side dish is sure to be a BIG HIT.

This easy recipe for cheesy spaghetti squash casserole adds a touch of fun to Thanksgiving dinner or any fall meal. It's a scrumptious swap for starchier side dishes that keto-friendly and gluten-free friends will love.
And if you transform it into a mini casserole cups, everyone, especially kids, will get excited about their veggies... because who can resist their own single-serving "muffin?"
It's a lesson we learned when making cauliflower cheese muffins and broccoli muffins.
By the way, "au gratin" isn't just a fancy term; it's a promise of golden, bubbly cheese crowning each serving. So spaghetti squash cups aren't just adorable; they're a cheese-lover's dream.

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Ingredients
Below are the ingredients you'll need to make this spaghetti squash au gratin recipe:
- Strands of spaghetti squash - See the section below for several easy ways to cook spaghetti squash.
- Sour cream adds to the creamy texture. Use plain Greek yogurt for an extra boost of protein.
- Eggs help the casserole to hold its shape.
- Onion is diced and softened.
- Cheddar cheese - Sharp cheddar cheese is a nice contrast to the mild flavors in this casserole.
- Garlic powder adds a subtle flavoring to the dish.
- Olive oil is used to saute the onions.
- Salt and pepper
Please refer to the recipe card below for the full list of ingredients and detailed instructions.
How to Make Spaghetti Squash Strands
The biggest task in making any recipe with spaghetti squash, including spaghetti squash au gratin, is cooking it. But there are several easy methods, and you can take this step several days ahead.
You'll need about 4 cups of spaghetti squash strands to make 6 servings of this recipe. One medium-sized spaghetti squash should be enough.
Prep the Gourd (Any Method)
Stab the outside of the gourd with the tip of a sharp knife to allow steam to escape while cooking. Make at least 10 cuts or more for larger gourds.
If you plan to cut the spaghetti squash in half before you cook it, place the squash (that's been poked) on a microwave-safe plate and cook in the microwave for 1-2 minutes. This will make it easier to cut the spaghetti squash in half.
Cook Whole Squash (Oven or Slow Cooker)
You can cook spaghetti squash whole in the oven or a slow cooker. It's simple to do. And once the squash is cooked, it's EASY to cut the gourd in half.
Here's the easy process:
- Place the prepped spaghetti squash in a slow cooker and cover. Or place it in an oven preheated to 425°F on a baking sheet.
- Slow cooker: Cook on low for 5-6 hours or high for 3-4 hours or until a knife can be easily inserted into the gourd.
- Oven: Roast for about 30 minutes, rolling over halfway through.
- Allow spaghetti squash to cool for about 10 minutes. Cut in half and remove seeds. Scrape the spaghetti squash strands from the insides of the squash halves.
Cook Halves in the Oven
This is the traditional method for cooking spaghetti squash:
- Cut the spaghetti squash in half and scoop out the seeds.
- Brush the inside with olive oil and season with salt and pepper.
- Place squash halves, flesh side down, on a sheet pan lined with aluminum foil.
- Bake for 40 minutes in a 375°F oven or until the flesh is tender to touch.
- Use a fork to remove the strands.
Directions with Pictures
Spaghetti squash au gratin is easy to make once you've scraped the strands from the gourd. We'll show you how to make a traditional casserole in an 8 x 10 dish or muffin pan.
- Heat olive oil in a skillet over medium heat. Add diced onion and saute for about 5 minutes or until tender.
- Add strands of spaghetti squash, cooked onions, sour cream, garlic powder, salt, eggs, and half of the cheddar cheese to a large bowl and mix to combine.
- Drain excess liquid from the spaghetti squash strands first. But there's no need to go crazy squeezing and pressing out the wetness for this recipe.
- Spread the mixture into a buttered baking dish (8 x 10) or portion the mixture into a regular-sized muffin pan (will make 18 muffin-sized servings.)
- Spritz with non-stick spray first.
- Sprinkle the remaining cheese over the top.
- Bake for about 25 minutes, then turn the oven to broil and cook for about 2 minutes more or until the top is golden brown.
Allow the spaghetti squash muffins to cool for 5-10 minutes.
Muffin Pan Method
The steps are the same to prepare the spaghetti squash mixture to be cooked in cups, except that everything is portioned into a cupcake or muffin pan.
As with the casserole version, it's very important to allow at least 10 minutes for the dish to set.
Use a nylon spatula to carefully remove spaghetti squash au gratin casserole cups to a serving platter.
Storage and Make Ahead Tips
Refrigerator: Store leftover spaghetti squash au gratin in an airtight container for up to 3 days.
Make Ahead: There are several make-ahead options:
- Cook the spaghetti squash ahead of time and refrigerate the spaghetti strands until you are ready to make the recipe (up to 5 days.)
- Prepare the recipe the day before and cook the next day.
- Prepare and cook the recipe and heat it up the next day.
Freezer: You can make this recipe and freeze it before or after cooking it!
- If already cooked, reheat the casserole or cups in a 350°F oven so that the internal temperature reaches 145°F. We do not recommend using the microwave.
- To freeze this recipe uncooked, prepare it, then tightly cover and freeze for up to 2 months. Defrost overnight in the refrigerator and cook as usual.
Variations
Here are some more ideas to take spaghetti squash au gratin to the next level or turn it into a meal:
- Caramelize the onions instead of just softening them.
- Add red pepper flakes for some heat.
- Add chicken (up to 1 cup diced or shredded) to turn this into a main dish.
- Add bacon (up to 1 cup crumbled.)
- Make spaghetti squash boats! Once you've removed the strands and mixed everything together, return it to the inside of the empty gourd and bake.
More Spaghetti Squash Recipes
Would you like more easy, healthy, carb-conscious recipes?
📋 Recipe
Spaghetti Squash Au Gratin Casserole or Cups
Ingredients
- 4 cups spaghetti squash strands, cooked 1 medium spaghetti squash; see notes and section above for cooking methods
- 1 teaspoon olive oil
- 1 cup onion 1 small onion; diced
- ½ cup sour cream or Greek yogurt
- 1 cup cheddar cheese shredded; divided
- 2 eggs lightly beaten
- ½ teaspoon garlic powder
- ¼ teaspoon salt or to taste
Instructions
- Preheat oven to 350°F.
- Measure out 4 cups of spaghetti squash strands, draining off any excess liquid, and set aside.
- Heat olive oil in a small skillet over medium heat. Add diced onion and saute for about 5 minutes or until tender.
- Add cooked onion, strands of spaghetti squash, sour cream, ½ cup of cheddar cheese, whisked eggs, garlic powder, and salt to a large bowl and mix to combine.
- Spread the mixture into an 8 x 10 casserole dish or regular-sized muffin pans sprayed with non-stick cooking spray (will make 18 au gratin cups.)
- Sprinkle remaining cheddar cheese over the top of the spaghetti squash mixture.
- Bake for about 25 minutes or until firm and starting to brown on top.
- Turn oven to broil and cook for 2-3 minutes more to crisp the tops.
- Allow spaghetti squash au gratin to cool for 10 minutes before serving.
Notes
- Use Greek Yogurt instead of sour cream for more protein.
- To cook spaghetti whole:
- Stab the outside gourd with a sharp knife to allow steam to escape while cooking. Insert knife tip about ½ an inch. Make at least 10 cuts or more for larger gourds.
- Place spaghetti squash in a slow cooker and cover or place in the oven preheated to 425°F on a baking sheet.
- Slow cooker: Cook on low for 5-6 hours or high for 3-4 hours or until a knife can be easily inserted into the gourd.
- Oven: Roast for about 30 minutes, rolling over halfway through.
- Allow the spaghetti squash to cool for about 10 minutes. Cut in half and remove seeds. Scrape the spaghetti squash strands from the insides of the squash halves with a fork.
- To cut in half and then cook:
- Cut the spaghetti squash in half and scoop out the seeds.
- Brush the inside with olive oil and season with salt and pepper.
- Place squash halves, flesh side down, on a sheet pan lined with aluminum foil.
- Bake for 40 minutes in a 375°F oven or until the flesh is tender to touch.
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- There are several options to make the recipe ahead of time:
- Cook the spaghetti squash ahead of time and refrigerate the spaghetti strands until you are ready to make the recipe (up to 5 days.)
- Prepare the recipe the day before and cook it the next day.
- Prepare and cook the recipe and reheat it the next day.
- Freezer options:
- To freeze this recipe uncooked, add everything to a freezer-safe dish, cover tightly, and freeze for up to 2 months. Defrost overnight in the refrigerator and cook as usual.
- If already cooked when frozen, reheat the casserole in a 350°F oven so that the internal temperature reaches 145°F. We do not recommend using the microwave.
- For either option, tent with foil if browning too quickly.
Shelley says
Hi
Can these be made a day ahead and reheated?
Marjory Pilley says
Yes they can! For the best result pop them back in the oven. See the storage and reheating section for more details.
Stefanie says
Maybe a dumb question, but how do you cook spaghetti squash strands? Do you boil them the same as regular spaghetti?
Marjory Pilley says
Hi! Check out the link on cooked spaghetti squash in the ingredients section or check out the expert tips and notes below the instructions. Either cook it in a slow cooker (I love this method) or bake in the oven!
Haley says
Hi friend!
Yummiest and looking awesome. Can't wait to try it.
It's looks amazing and I think it made easily. What happen if not add sour cream in it?
Thanks.
Marjory Pilley says
Hi! You can leave the sour cream out! It's a slightly different flavor profile. You can also substitute with cream cheese.