Spaghetti Squash Au Gratin Casserole or Cups

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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.

Jump to:

• Ingredients
• How to Make Spaghetti Squash Strands
• Directions with Pictures
• Storage and Make Ahead Tips
• Variations
• More Spaghetti Squash Recipes
• 📋 Recipe

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:

1. 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.
2. 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.
3. Oven: Roast for about 30 minutes, rolling over halfway through.
4. 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:

1. Cut the spaghetti squash in half and scoop out the seeds.
2. Brush the inside with olive oil and season with salt and pepper.
3. Place squash halves, flesh side down, on a sheet pan lined with aluminum foil.
4. Bake for 40 minutes in a 375°F oven or until the flesh is tender to touch.
5. 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.

1. Heat olive oil in a skillet over medium heat. Add diced onion and saute for about 5 minutes or until tender.
2. 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.
3. 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.
4. Sprinkle the remaining cheese over the top.
5. 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

📋 Recipe