Spaghetti Squash Muffins (Au Gratin Cups)

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Make Spaghetti Squash Muffins au gratin style in cute little cups. This cheesy, low-carb, healthy side dish will be a BIG HIT at the dinner table!

The unconventional presentation of healthy spaghetti squash au gratin casserole in the shape of a muffin is guaranteed to make an impression! 

• It's a tasty alternative to starchier side dishes. Hello low-carb or gluten-free friends!
• It's kid-friendly! Who doesn't like little veggies shaped into muffin-sized bites?
• They're packed with protein, especially if you make it with Greek yogurt!

Healthy Vegetable Muffins or "cups" have become a staple around here. From Cauliflower Muffins to Spinach and Feta Muffins, we are on a mission to make eating vegetables easy and fun.

This recipe is fancy enough for your Thanksgiving dinner or fall table. But it's also easy enough to snack on year-round!

In case you're wondering, au gratin simply means that cheese (or bread crumbs) has been sprinkled on top and browned. Yet, another reason to love these cute little spaghetti squash muffins...they're topped with extra cheese!

Jump to:

• How to Cook Spaghetti Squash
• Directions
• Storage and Make Ahead Tips
• Variations
• More Spaghetti Squash Recipes
• 📋 Recipe

How to Cook Spaghetti Squash

The biggest obstacle to making any recipe with spaghetti squash is cooking the squash. However, it's only a burden if you struggle to cut it in half before you cook it!

Luckily, you don't have to!

Cook spaghetti squash whole in the oven or slow cooker. It's simple to do and you can take this step days ahead of time! Once the squash is cooked, it's EASY to cut.

You'll need about 4 cups of spaghetti squash strands to make 6 servings of this recipe. One medium-sized spaghetti squash should do the trick. 

Here's the easy process:

1. Stab all over the outside gourd with a knife to allow steam to escape while cooking. Insert the tip about ½ an inch. Make at least 10 cuts or more for larger gourds.
2. Place spaghetti squash in a slow cooker and cover or place in the oven preheated to 425 °F on a baking sheet.
3. 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.
4. Oven: Roast for about 30 minutes, rolling over halfway through.
5. Allow spaghetti squash to cool for about 10 minutes. Cut in half and remove seeds. Scrape spaghetti squash strands from the gourd with a fork.

Directions

Once the squash is cooked, spaghetti squash muffins au gratin are easy to make!

Remove strands of spaghetti squash from the gourd with a fork and drain off any excess liquid. No need to go crazy squeezing and pressing out the wetness for this recipe!

Next, combine the main ingredients:

• Strands of spaghetti squash
• Sauteed onions - dice and cook in olive oil for about 5 minutes to soften
• Garlic powder
• Sour cream or Greek Yogurt
• Cheddar cheese - shredded
• Eggs

Scoop the mixture into a muffin pan sprayed with non-stick cooking spray OR an 8x10 baking dish if you're making a traditional casserole. 

Sprinkle more cheese on top!

Bake for about 25 minutes, then turn the oven to broil and cook for about 2 minutes more to brown the tops.

Allow the spaghetti squash muffins to cool for 5-10 minutes.

Use a nylon spatula to carefully remove spaghetti squash au gratin casserole cups to a serving platter. Note that spaghetti squash cups are less firm and more "eggy" than our veggie-packed muffins. 

Storage and Make Ahead Tips

Refrigerator: Store muffins in a sealed container for up to 3 days.

Make Ahead: There are several make-ahead options for spaghetti squash egg cups:

• 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 up and freeze it before or after cooking it!

• If already cooked, reheat the muffins in a 350 °F oven so that the internal temperature reaches 145 °F. We do not recommend using the microwave to reheat muffins. 
• To freeze this recipe uncooked, add everything to a freezer-safe plastic bag that seals. Leave the cheese that goes on top off. Defrost the mixture overnight in the freezer when you are ready to cook the recipe. Then, start with Step 4 below and finish the recipe. This is the same method we use to make ahead and freeze crustless quiche.

Variations

Here are some more ideas to take spaghetti squash muffins to the next level or turn them into a meal:

• Caramelize the onions instead of just softening them.
• Use whipped cream cheese instead of sour cream or yogurt.
• Add red pepper flakes for some heat.
• Add chicken (up to 1 cup diced or shredded.)
• Add bacon (up to 1 cup crumbled.)

Looking for a plant-based version? Check out Creamy Vegan Spaghetti Squash Bake by Spoon Fork Bacon.

More Spaghetti Squash Recipes

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