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!
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


  • 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


  • 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.



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.


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