Spaghetti Squash Au Gratin

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This Spaghetti Squash Au Gratin packed with a combination of Gruyere and Parmesan cheeses with garlic, onion, and fresh herbs is absolutely delicious and surprisingly healthy,

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One of my favorite winter vegetables is spaghetti squash. While that may seem like a strange choice, hear me out, as it can be incredibly versatile and useful in many recipes. It's also easy to cook, good for you, and makes a great low-carb replacement in many dishes where you'd typically use pasta.

I admit I was skeptical of the squash at first as well. I mean, it looks so meh. But then, I learned how great it tastes and how healthy it is for you. It's full of vitamins and minerals that you need to get you through those cold winter months.

One of my go-to recipes for spaghetti squash involves creating a warm, cheesy gratin. It makes a great dish with a soup or salad side, or it makes a perfect side as well. You can also make this same recipe with shredded zucchini or summer squash.

Spaghetti squash au gratin with fresh Parmesan and basil in a dish with two forks.

What is au gratin?

So for so long, I thought that a gratin was relegated specifically to a potato dish. I didn't know that the "gratin" actually refers to the technique of browning a crust. So you can "gratin" lots of things — potatoes, squash, or a breadcrumb, butter, and cheese mixture — I suppose you could get pretty creative here.

Gratins are also typically made in shallow dishes and are cooked in a broiler so that crust can form. It's also usually served right in the dish in which it was baked.

What makes Spaghetti Squash Gratin healthy?

  • Spaghetti squash is a low-calorie, low-fat, and low-carb food. It has 1 gram of protein per 1 cup serving, 2 grams of fiber, and 4 grams of sugar. It contains fiber, folate, potassium, calcium, omega-3s and -6s, iron, zinc, and B vitamins.
  • Onions contain sulfites which contain necessary amino acids. They also offer fiber and folic acid, which is good for growing healthy new cells. You can eat them raw or cooked and still reap their health benefits.
  • Garlic is a great source of antioxidants, and it's also antimicrobial and great for your heart. Some studies have shown that garlic can also help lower cholesterol levels, regulate blood pressure, and regulate your blood sugar.
  • Eggs are a great high-quality protein source, especially when you eat the whites. They are inexpensive and so versatile. They also contain vitamins B2, D, B6, and B12. The egg whites are low in fat, but the fat in eggs is nothing to be concerned about if eaten in moderation. Eggs also are a great source of copper, iron, zinc, and selenium.
  • Skim milk is a great way to get in all that milk protein and calcium while eating a lower-fat and lower-calorie version than whole milk.
  • Basil is widely used for its spicy, herby flavor. But it also is a great source of magnesium and helps to promote good circulation. It also is a great source of multiple vitamins such as A, which has been shown to be healthy for your eyes. It's also used as an anti-inflammatory.
  • Hard cheeses such as Parmesan and Gruyere are lower-fat, nuttier-tasting cheeses that add that great cheesy taste you want without a ton of fat and calories. They are also a great protein and calcium source as well.

Is Spaghetti Squash Keto-Friendly?

The short answer is yes, spaghetti squash is a low-carb option, and therefore Keto-friendly. It's a great replacement for other starches that are high in carbs, such as potatoes, pasta, and other grains.

Au gratin with spaghetti squash, basil, garlic, onions, and melted cheese in a baking dish.

How can I customize Spaghetti Squash Au Gratin?

  • Add diced, cooked bacon to the squash mixture before topping with cheese and cooking.
  • Switch up the herbs to suit your tastes. Try chives, thyme, rosemary, or oregano to mix up the flavor profile.
  • If you want to make it spicy, consider adding some diced, jarred jalapeno slices to the squash mixture. Or, top with salsa or hot sauce.
  • Mushrooms work well in this dish too, just be sure to cook them separately and drain off excess water so to keep the gratin from being too soggy.
  • You could mix up the squashes you use in your gratin as well. Use all spaghetti or a combo of spaghetti, zucchini, and yellow squash to vary the flavor and textures.
  • Take this dish in a Mexican direction, taking inspiration from these Spaghetti Squash Burrito Bowls, with pepper jack, salsa, and your favorite taco toppings.

Can I cook the spaghetti squash in the microwave?

If you want to speed things up, consider cooking the spaghetti squash in the microwave. Start by piercing the spaghetti squash all over with a fork. Then place the whole squash on a microwave-safe plate and microwave for 10-14 minutes (depending on size) until the squash is tender. Carefully cut in half once it has cooled slightly, being careful of the steam. Remove the seeds and scrape out with a fork.

No matter how you choose to make this gratin, I'm sure you'll love it and grow to be a spaghetti squash convert like I am!

Looking for more spaghetti squash recipes?

The Recipe
Spaghetti squash gratin in a glass baking dish with parmesan cheese and basil.

Spaghetti Squash Au Gratin

TOTAL TIME: 1 Hours, 30 Min
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  • 1 spaghetti squash
  • 1 onion, diced
  • 2 garlic cloves, minced
  • 3 eggs
  • 1/2 cup skim milk
  • 2 tbsp fresh basil, chopped
  • 1/2 cup Gruyère cheese, shredded
  • 2 tbsp Parmesan cheese
  • 1 salt and freshly ground pepper

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Preheat your oven to 375 degrees. Cut your spaghetti squash in half and scoop out the seeds. Spray with non stick cooking spray and place flesh side down on a baking sheet covered in foil. Let cook for 45 minutes or until squash is cooked through and tender. Let squash cool and once it has, pull out the spaghetti squash with a fork. Chop the squash into smaller pieces and measure out 4 cups.


Spray a non stick pan with cooking spray and sauté and onions and garlic until translucent and fragrant. Add the spaghetti squash and cook for an additional 3-4 minutes. Add salt and pepper to taste.


Beat the three eggs in a large mixing bowl. Add the milk, cheese, basil, and salt and pepper and mix together. Add the squash and stir together.


Spray an 8 or 9 inch pie plate or casserole dish with cooking spray and add in egg, cheese, basil, and squash combination.


Sprinkle the top with the Parmesan cheese.


Bake for 40-45 minutes until the top is golden brown.

Nutritional Facts
Serving Size: 1 slice (205g)
Amount Per Serving
Calories 82
Calories from Fat 34
% Daily Value *
Total Fat 4g
Saturated Fat 2g
Monounsaturated Fat 0g
Polyunsaturated Fat 0g
Cholesterol 75mg
Sodium 87mg
Total Carbohydrate 7g
Dietary Fiber 1g
Sugars 3g
Protein 5g

* Percent Daily Values are based on a 2,000 calorie diet. Your daily values may be higher or lower depending on your calorie needs.

The Nutritional Values provided are estimates only and may vary based on the preparation method.

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About the author Meet Kristen McCaffrey
Hi, I’m the cookbook author, recipe developer, and food enthusiast behind Slender Kitchen. I am obsessed with making healthy food that is easy to prepare and absolutely delicious. Meal planning is my secret weapon and I hope I can make meal time easier for you with our tried and tested recipes and foolproof meal plans. Learn More
1 Comment
On Spaghetti Squash Au Gratin
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December 20, 2019 - 14:12
can I used plant based milk instead of cow milk?
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