Warning! This Spaghetti Squash Gratin includes dairy. If you follow a strictly dairy-free diet, this recipe may not be for you—it’s a decadent, hard-to-resist dish.

If you’re still reading, I’ll assume you enjoy dairy occasionally. Some people describe diets that include limited dairy as “primal,” so this recipe is best called a Primal Spaghetti Squash Gratin.

The star dairy in this gratin is one of the finest melting cheeses: Gruyère.

Gruyère is a classic Swiss cheese with a creamy, nutty, and slightly earthy flavor—it’s the same cheese that makes French onion soup irresistible. When used in a gratin, authentic Swiss Gruyère offers a richer, more complex taste than many domestic substitutes, and a little goes a long way.

This gratin is especially comforting on cool autumn and winter evenings. The spaghetti squash retains a slight bite while the nutmeg highlights the Gruyère’s warmth. Serve it alongside steak and a green salad or as a cozy substitute for traditional macaroni and cheese.
Primal Spaghetti Squash Gratin
Spaghetti Squash Gratin (Primal & Gluten-free)
Gratin made with spaghetti squash — a flavorful, comforting side dish.
- Author: Lea Valle
- Category: side
Ingredients
- 1 spaghetti squash
- 2 tablespoons butter
- 1 medium onion, finely diced
- 3/4 cup plain Greek yogurt
- 1 1/4 cup grated Gruyère cheese (divided)
- 1 1/2 – 2 teaspoons sea salt (to taste)
- 1/2 teaspoon black pepper
- 1/4 teaspoon grated nutmeg
Instructions
- Preheat the oven to 375°F (190°C).
- Cut the spaghetti squash in half lengthwise and place rind side up on a baking sheet. If the squash is hard to cut, microwave each half for a couple of minutes to soften slightly. Pour about 1/4 inch of water into the pan, then bake for 45 minutes. Allow the squash to cool until it’s safe to handle.
- Scoop out and discard the seeds and membranes from each half.
- Use a fork to shred the flesh of the squash into strands, then set aside.
- In a medium or large skillet, melt the butter over medium heat.
- Add the finely diced onion and sauté until translucent, about 10–12 minutes. Stir in the salt, pepper, and nutmeg.
- Stir in the Greek yogurt, shredded spaghetti squash, and 3/4 cup of the grated Gruyère. Heat for a couple of minutes until well combined and warmed through.
- Transfer the mixture to a baking dish and spread it evenly.
- Sprinkle the remaining 1/2 cup of Gruyère over the top and bake for 30 minutes, until hot and bubbling. If the top isn’t nicely browned, broil on high for a few minutes—watch closely so the cheese doesn’t burn—to toast the Gruyère.
Ingredients
- 1 spaghetti squash
- 2 tablespoons butter
- 1 medium onion, finely diced
- 3/4 cup plain Greek yogurt
- 1 1/4 cup grated Gruyère cheese (divided)
- 1 1/2 – 2 teaspoons sea salt (to taste)
- 1/2 teaspoon black pepper
- 1/4 teaspoon grated nutmeg
Instructions
- Preheat oven to 375 degrees F.
- Cut the squash in half lengthwise and place rind side up on a baking sheet. (If needed, microwave briefly to soften before baking.) Pour enough water into the pan to reach about 1/4 inch, bake for 45 minutes, and let cool.

- Scoop out seeds and membranes from each half. I find this easiest after baking.

- Shred the squash flesh with a fork and set aside.
- Melt butter in a medium/large pan.

- Sauté the diced onions until translucent, about 12 minutes. Stir in salt, pepper, and nutmeg.
- Add Greek yogurt, the shredded squash, and 3/4 cup Gruyère to the pan. Stir to combine and heat for a few minutes over medium heat.
- Transfer the mixture to a baking dish and spread evenly.

- Top with the remaining 1/2 cup grated Gruyère and bake for 30 minutes, until bubbling. Broil briefly if you want a golden, toasted top.
Serves 8–10
Enjoy!

What do you think? Will you try this primal spaghetti squash gratin?
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