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 Veggie 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!
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How to Cook Spaghetti Squash
The biggest obstacle to making any recipe that uses spaghetti squash is cooking the squash. It's only a burden if you struggle to cut it in half before you cook it!
However, 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:
- Stab all over the outside gourd with a knife to allow steam to escape while cooking. Insert tip about ½ and 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 in the outside.
- 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 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 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 au gratin to the next level or turn it 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 Vegetable Muffins
Did you make this recipe?
Please leave a rating and tell us how you liked it!
📋 Recipe
Spaghetti Squash Muffins - Au Gratin Cups
Ingredients
- 1 teaspoon olive oil
- 1 cup onion 1 small onion; diced
- 4 cups spaghetti squash strands, cooked 1 medium spaghetti squash; see notes and section above for cooking whole in the oven or a slow cooker
- ½ teaspoon garlic powder
- ½ cup sour cream or Greek yogurt
- 1 cup cheddar cheese shredded; divided
- 2 eggs large or extra-large; lightly beaten
Instructions
- Preheat oven to 350 °F.
- Heat olive oil in a skillet over medium heat. Add diced onion and saute for about 5 minutes or until tender.
- Add cooked onion, strands of spaghetti squash, garlic powder, sour cream, ½ cup of cheddar cheese and eggs to a large bowl and mix to combine.
- Portion mixture into regular-sized muffin pans sprayed with non-stick cooking spray (will make 18 cups) (or an 8 x 10 casserole dish.)
- 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 if desired to crisp the tops.
- Allow spaghetti squash au gratin to cool for 5-10 minutes before serving.
Notes
- Use Greek Yogurt for South Beach Diet Phase 1 Diets
- To cook spaghetti whole:
- Stab all over the outside gourd with a knife to allow steam to escape while cooking. Insert tip about ½ and 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 in the outside.
- 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 spaghetti squash strands from the gourd with a fork.
- 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 re-heat it the next day.
- Freezer options:
- 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 and finish the recipe.
- 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 to reheat muffins.
- For either option, tent with foil if browning too quickly.
Haley
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
Hi! You can leave the sour cream out! It's a slightly different flavor profile. You can also substitute with cream cheese.
Stefanie
Maybe a dumb question, but how do you cook spaghetti squash strands? Do you boil them the same as regular spaghetti?
Marjory Pilley
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!