Spaghetti Squash Gratin (Primal & Gluten-free)

Spaghetti Squash Gratin:

Warning! The recipe for Spaghetti Squash Gratin contains dairy ingredients. This one is going to be hard to resist. So if you are strictly dairy-free you might want to stop reading now. Spaghetti Squash Gratin

Okay, if you are still reading I will assume you eat dairy products from time to time.

Minimally, I hope you are not inclined to inform me in the comments the paleo diet does not include dairy. (Actually, yes it does depending on your tolerance and the type of dairy. But let’s not argue. Okay?)

Perhaps we can agree on the term “primal” which is typically used to describe a paleo diet or recipe that does include some dairy products. So let’s agree the following recipe is a Primal Spaghetti Squash Gratin.

spaghetti squash gratin by

The dairy in this spaghetti squash gratin is not just any old dairy, it’s one of the most wonderful cheeses known to mankind.

I’m talking about Gruyère cheese.

Gruyere cheese for primal spaghetti squash gratin

If you have never tried Gruyère you are really missing out. Gruyère is a type of Swiss cheese. This is the same cheese found atop high quality French onion soup. When added to a gratin it imparts a simply amazing flavor. And, in my experience, it is worth splurging on the original version made in Switzerland as opposed to domestic U.S. varieties. The flavor of the original Gruyère is unsurpassed and you need less of it to get the characteristic creamy, nutty, earthy and complex flavor in a recipe.

Spaghetti Squash Gratin

This dish is great on chilly autumn and winter days. The spaghetti squash still has a slight crunch and the nutmeg accents the Gruyère perfectly. It would be delicious with steak and a salad or really any meal that you may, in the past, have served with (God forbid) Macaroni & Cheese.

Primal Spaghetti Squash Gratin


  • 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



  1. Preheat oven to 375 degrees F.
  2. Cut it in half lengthwise and place rind side up on a baking sheet. (If you have trouble cutting the squash you might consider microwaving for a couple of minutes just to soften a bit before baking.) Pour enough water in the pan to come up about 1/4”. Bake for 45 minutes and allow to cool.spaghetti squash gratin
  3. Scoop out the seeds and membranes from each side of the squash. (I find it easier to do after baking but some people do it before)baked spaghetti squash
  4. Use a fork to “shred” the flesh of the spaghetti squash -set aside.
  5. Heat butter in a medium/large pan. Mmmm butter….melting butter
  6. Add the finely diced onions to the pan and sauté until translucent (approximately 12 minutes). Stir in the salt, pepper and nutmeg.
  7. Add the Greek yogurt, spaghetti squash and 3/4 cup of the Gruyère to the pan, stirring to combine, and heat for a couple of minutes on medium.
  8. Pour the mixture into a baking dish and spread it evenly.spaghetti squash in baking dish
  9. Top with the remaining 1/2 cup of grated cheese and bake for 30 minutes until hot and bubbling. If the top is not browned you can broil on high for a few minutes until the Gruyère cheese is nicely toasted.

Serves 8-10


Spaghetti Squash Gratin:

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

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37 thoughts on “Spaghetti Squash Gratin (Primal & Gluten-free)

  1. I can tolerate a little dairy so I think I will try this! I like your Mac and Cheese (God forbid) comment. Made me chuckle. Before I went paleo, though I ate pretty well, I did indulge once on a while on a (gasp) frozen side dish of Trader Joes Frozen Mac and Cheese and it had gruyere cheese in it. It was to die for! I am hoping this will taste a little like it….and I love spaghetti squash. Thanks for the recipe. Have a great day. Off to do my at home WOD since my DS is home with a cold…poor kid.

    • Hi Debbie,
      I’m very familiar with Trader Joe’s frozen Mac & Cheese. Before paleo we didn’t eat a ton of pasta but we definitely had that dish from time to time. I’m not sure what I would think if I were to try it again. I’m honestly not tempted by starchy pastas and breads anymore. This dish should be reminiscent of it but obviously will be very different. I hope you like it. And I hope your little one feels better soon!
      Take care, Lea

  2. I have one spaghetti squash left over from my summer garden – it’s going in this recipe tomorrow! Can’t wait to try it out!

  3. I am as Paleo as a girl can get, but seriously, this is it. I am going to try this one, cheese and diary pro or contra. This is such a great and simple recipe and idea, I am sure it will taste amazing. Cannot wait to try it, thank you for this great recipe!

  4. Two questions:
    1. Can I use plain whole milk yogurt instead of plain Greek yogurt?
    2. Can I skip the microwave step and just cook the spaghetti squash a little longer in the oven?
    Thanks a lot.

  5. What a fabulous recipe idea! I absolutely adore it. :) I’m so used to imagining only two ways to eat spaghetti squash (slathered in butter with salt & pepper, or topped with marinara sauce) that this simple and delightful way to prepare would never have occurred to me.

    Thank you!

    • You’re welcome Kristen. And thank you for the compliments and for linking to the recipe! I literally went to the grocery store today to buy more spaghetti squash and Gruyere just to make this again.

  6. We’ve been eating spaghetti squash with a simple cream and parm alfredo sauce with chicken and bacon… but this sounds like a fabulous version for eating with Christmas dinner! I cant wait to try it!

    • Well, Karen, I certainly can’t argue with the idea of adding bacon to a spaghetti squash recipe. That sounds good too. I hope you like this version.

  7. This was fantastic! I used 3 tablespoons of butter, just because I love it and added sautéed garlic, about 4 gloves chopped. I LOVE garlic; their isn’t much I don’t add garlic to! I will definitely be making it again!

  8. Mine turned about wonderful all three times I have made it! I wanted to let you know about my ‘happy accident’ that I stumbled upon. When I picked up yogurt, I thought it was plain until I checked the container, after dropping it in, and realized it was honey-flavored. I start to freak out then thought, a little sweetness couldn’t hurt, and I have to say I love it even better this way!

    I also like the comment about adding some garlic-you can’t go wrong with sauteed onions AND garlic :)
    Thanks for a delicious recipe for even non-spaghetti squash lovers!

  9. Lea, thank you for this wonderful recipe. Gruyere is on my shopping list for Friday and I can’t wait to try this! I will write after we give it a try. I did want to mention the most underutilized part of almost any squash….the seeds! I cut my squashes in half and scoop out the insides, clean off the seeds and add sea salt or spices to them. I then roast them on a piece of tinfoil alongside the squash for about 20 minutes, stirring every 5 minutes to keep them from sticking. Fabulous, yummy, nutritious little snack!

  10. This dish is absolutely delicious! We make this at least once a week and when we have dinner guests over. I agree that I do not miss pasta/starches at all since going Paleo but this recipe has really curbed any urge. It is nice to have a side dish that doesn’t feel so vegetable-y. Thank you so much for sharing!!

  11. I have made this twice and love love love it!!!! I am on the wheat belly diet so I can have cheese so this was not a problem for me. I made it once for a group of people and had no leftovers and people were talking about it all night. Will definitely make again!

    • I’ve never frozen it so I can’t make any guarantees. But I don’t see why it wouldn’t be just fine frozen and then eaten at a later time. Good luck.

  12. According to the time magazine “Nature”, the Paleo people ate cheese ;) And certain places drank cow / goat etc milk as well, when there was times with low food conditions… That should especially count for the more northern people in cold climates, as they still today, seem to cope with milk better than many others.

  13. Just wanted to say this has become a weekly staple at our house and we love it. We sometimes add ham and chicken and its a bit like chicken cordon blue. Great recipe

  14. Hi just made this wonderful creation, and being dairy intolerant but can do goat products I made this recipe with goat yogurt and goat cheese and it taste divine. MJ

  15. I’ve found our Mac & Cheese replacement for Thanksgiving dinner! I can only eat raw cheese, soft, and semi-soft cheeses, so will go with raw cheddar, havarti, and ricotta. I’m sure it will be delish. Hope everyone else thinks so…

  16. I made this last week and it was delicious! Do you have any tips on minimizing the liquid once it bakes? When you serve a piece there is generally some liquid in the bottom of the dish. Any suggestions would be great! Once again, the recipe is AMAZING!

    • Rachel,
      If you have too much liquid in the finished dish then you might want to consider wringing more liquid out of the cooked spaghetti squash. You can try using a clean dish towel for this and just wrap it inside and wring out some of the liquid. I think that will help the final product be drier for you.
      Good luck!, Lea

  17. Made this on Easter, absolutely delicious and an impressive dish!!! It is now one of my favorite family gathering recipes! Making it again this weekend.

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