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Soups, Salads & Sides » Sides » Spaghetti Squash Au Gratin Casserole or “Cups”

Spaghetti Squash Au Gratin Casserole or “Cups”

UPDATED Nov 26, 2019 · PUBLISHED Nov 26, 2019 BY Marjory Pilley · This post may contain affiliate links. As an Amazon Associate I earn from qualifying purchases.

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Recipe - Print - Video
Spaghetti Squash Au Gratin Casserole Cups stacked on a serving platter

Make Spaghetti Squash Au Gratin in a traditional casserole dish or cups. Either way, this cheesy, low-carb side dish will be a BIG HIT at the dinner table!

Two Spaghetti Squash Au Gratin cups on a plate

The unconventional presentation of this 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!

How to Cook Spaghetti Squash

The biggest obstacle to making this recipe…or 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. 

If you want to roast cut squash in the oven, then check out Spaghetti Squash Alfredo, where you can see the instructions and process shots.

Cooked whole spaghetti squash in a bowl in front of slow cooker

How to Make Spaghetti Squash Au Gratin Casserole or Cups

Once the squash is cooked, this spaghetti squash au gratin recipe is easy peasy!  

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 8×10 baking dish if you’re making a traditional casserole. 

Disher scoop portioning spaghetti squash au gratin mixture into pan

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 casserole or cups to cool for 5-10 minutes.

Baked Spaghetti Squash Au Gratin in muffin pan

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. 

FAQ

Can you make the recipe ahead of time?

Yes! 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.

Can you freeze spaghetti squash au gratin?

You can even make this recipe up and freeze it before or after cooking it!

  • If already cooked, reheat the casserole in a 350 degree Fahrenheit oven so that the internal temperature reaches 145 degrees Fahrenheit. 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.

Spaghetti Squash Au Gratin 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
  • 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.

Cheesy spaghetti squash au gratin cups stacked on plate with whole spaghetti squash in background.

Did you make this recipe? Please leave a rating and tag @DinnerMom or #DinnerMom on social media. We LOVE to see and share your creations!

Two rounds of Spaghetti Squash Au Gratin on a plate

Spaghetti Squash Au Gratin Casserole Cups

Make Spaghetti Squash Au Gratin in a casserole dish or pre-portion in cups! Either way, this cheesy, low-carb side dish will be a BIG HIT at the dinner table!
5 from 1 vote
Print Pin Rate
Course: Side Dish
Cuisine: American
Prep Time: 20 minutes
Cook Time: 25 minutes
Total Time: 45 minutes
Servings: 6 servings
Calories: 166kcal
Author: Marjory Pilley

Ingredients

  • 1 teaspoon olive oil
  • 1 cup onion 1 small onion; diced
  • 4 cups spaghetti squash strands, cooked 1 medium spaghetti squash; see notes for cooking whole in the oven or a slow cooker
  • 1/2 teaspoon garlic powder
  • 1/2 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 degrees 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, 1/2 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.

Video

Notes

Check out process pictures and more details above!
Expert tips and notes:
  1. Use Greek Yogurt for South Beach Diet Phase 1 Diets
  2. 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.
  3. 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 degree Fahrenheit oven so that the internal temperature reaches 145 degrees Fahrenheit. We do not recommend using the microwave to reheat muffins. 
    • For either option, tent with foil if browning too quickly.

Nutrition

Calories: 166kcal | Carbohydrates: 7g | Protein: 8g | Fat: 12g | Saturated Fat: 7g | Cholesterol: 84mg | Sodium: 162mg | Potassium: 156mg | Fiber: 1g | Sugar: 3g | Vitamin A: 445IU | Vitamin C: 3mg | Calcium: 182mg | Iron: 1mg
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Reader Interactions

Comments

  1. Haley

    November 26, 2019 at 8:46 pm

    5 stars
    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.

    Reply
    • Marjory Pilley

      November 27, 2019 at 7:35 am

      Hi! You can leave the sour cream out! It’s a slightly different flavor profile. You can also substitute with cream cheese.

      Reply

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