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Spaghetti Squash Au Gratin – Low Carb, Cheesy and Delicious

We enjoy this spaghetti squash au gratin recipe because it uses ingredients that we normally have on hand to make a yummy dish. The texture is rich and creamy, but with less carbs than scalloped potatoes.

spaghetti squash au gratin

My brother refers to spaghetti squash as “the tribbles of the garden”. When you have healthy plants, they can produce a LOT of squash. This year we had over 100 squash from one hill and a couple of volunteer plants. This left enough squash to share with the duckies, plus plenty to try out new recipes. Plant a whole package of seeds, and you may end up with enough squash to feed a small army.


Spaghetti Squash Au Gratin

This rich and creamy side dish gives you the comfort food taste you love without a ton of carbs.

  • Author: Laurie Neverman
  • Prep Time: 15 minutes
  • Cook Time: 75 minutes
  • Total Time: 1 hour 30 minutes
  • Yield: 15 servings 1x
  • Category: side dish
  • Method: baking
  • Cuisine: American


Units Scale
  • 1 medium spaghetti squash
  • 2 tablespoons butter
  • 1 medium onion, finely diced
  • 3/4 cup sour cream
  • 1 1/4 cup grated Parmesan cheese (divided)
  • 1 1/22 teaspoons sea salt (or to taste)
  • 1/2 teaspoon black pepper
  • 1/4 teaspoon grated nutmeg


  1. Cook your spaghetti squash. Preheat oven to 350°F. Slice spaghetti squash in half lengthwise and scoop out the seeds and pulp. Place squash cut side down in a large baking dish or roasting pan. Add water to cover bottom of pan. Place pan in oven and bake for 45 minutes.
  2. While the squash is baking, prep the rest of the ingredients. Shred the cheese. Set 1/2 cup of cheese aside.
  3. Chop the onions and saute them in the butter until translucent.
  4. Stir salt, pepper and nutmeg into the onions.
  5. Remove the squash from the oven and allow it too cool enough so that you can handle it. Shred the flesh of the spaghetti squash with a fork. Turn oven temp up to 375°F.
  6. Add the squash, sour cream and 3/4 cup of shredded cheese to the onion mix. Stir until evenly mixed.
  7. Spread the squash mixture into a 9×13 baking dish. Top with remaining 1/2 cup of cheese.
  8. Place pan in preheated oven and bake for 30-35 minutes, until top is lightly brown and cheese is bubbling.
  9. Serve warm. Refrigerate any leftovers.


Cook time includes initial baking time for squash. If you have an Instant Pot or similar pressure cooker, you can prep the squash in that cooker. Slice in half and remove seeds and pulp. Place a rack and one cup of water in the bottom of the pot. Close lid and cook the squash on High for 7 minutes. Carefully vent the cooker and test squash for doneness. Proceed with the rest of the recipe.

Keywords: spaghetti squash, au gratin, cheese, low carb

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    1. I’m glad it worked well for you, Jo Ann, and thanks for taking time to let me know. Positive comments on recipes make it more likely that search engines will recommend them, so it is very much appreciated.

  1. This looks delicious Laurie! Thanks for sharing.
    Spaghetti squash grows so prolifically here. Since I’m being careful with carbs these days, I’ve been cooking more with spaghetti squash as a pasta replacement. I look forward to trying this.

    1. I remember you mentioning how you used spaghetti squash regularly. We have never had as many as we had this year, so I’ve finally made my peace with them and am embracing the squashness. I still don’t find them to be a perfect one to one swap for pasta, but I am continuing to refine my cooking technique to get just the right levels of doneness for different uses. The less mature ones cook up quickly and tend to get mushy, so they aren’t great for a pasta-type texture, but the older, fully mature squash do better. Some of ours had to come in slightly underripe to avoid the frost and matured inside. The duckies are getting more of those, while we enjoy the firmer ones.

      1. Looks pretty yummy to me! Actually, I was a bit skeptical of spaghetti squash as a pasta sub. too, until I needed to cut all grains and pastas out! I tried it, and it really does act like pasta! I now love it as a spaghetti sub. But as I can’t have potatoes either, this could be a real winner for me!

  2. Longtime grateful subscriber. Thank y’all!
    Retired cancer survivor learning how to eat healthy for once and you’ve helped so much. Weird, I bought my first spaghetti squash couple weeks ago and cooked it and loved it but it didn’t have enough flavor, and boom, you put out this awesome recipe. Thanks again!