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Gooey, Creamy, Delectable Gluten-Free “Mac & Cheese” Baked Spaghetti Squash

The most delectable gluten-free mac & cheese substitute! Gooey, creamy baked "mac & cheese" spaghetti squash | Tasting Everything


An easy-to-make, gluten-free recipe for baked spaghetti squash that tastes exactly like macaroni and cheese, but is totally healthier? Could there be such a thing? I had to try!


*Update: Though I originally posted this recipe in the fall when squash was really in season, holidays are a time for comfort foods and this one is no exception. Because this is easily one of the more popular recipes from Tasting Everything on Pinterest, I decided to remind people out there that it’s here if they’re looking for a healthier holiday comfort food alternative!


Heavy, warm foods with flavors that remind me of my childhood really start to appeal to me as each new holiday approaches. And we are just entering the next holiday season, so it’s never too early for meal planning (and tasting!).

There is something about the summer turning into fall that makes me crave comfort foods. Heavy, warm foods with flavors that remind me of my childhood really start to appeal to me this time of year.  Soups, stews, braised meats and vegetables, confit anything… The list is pretty much endless! We are just entering that time of year that’s so perfect for decadent and glossy sauces, rich pastas and risottos, and any large part of an animal that has been  slowly roasted to falling-apart perfection.
Yesterday, mac and cheese sounded fantastic, but I had this spaghetti squash that I really wanted to use, so I made gluten-free “mac and cheese” baked spaghetti squash. The only thing that makes this different from a recipe with gluten is the flour. If you want a really tasty mac and cheese sauce but only have regular flour, just go ahead and swap out the gluten-free flour for what you have on hand.


I absolutely swear by the ATK gluten-free flour blend, but by all means use whatever gluten-free flour blend you have on hand. For a recipe that involves a roux – a mixture of butter and flour – I have had absolutely no problem switching in whatever gluten-free flour blend I have on hand. I’ve found a few differences in flavor, for example, one might be a little nuttier that another, but it’s really tough to tell them apart unless you’re doing a side-by-side comparison. All of the standard and readily available gluten-free blends that I’ve tried so far have worked perfectly for this application.

This mac and cheese sauce is one I’ve been playing with for years. It has a lot of the flavor of the boxed mac and cheeses that I grew up with, which I really enjoy! It actually has something to do with the combination of mustard powder, turmeric, and paprika. I did a lot of research a few years ago trying to recreate that flavor, and these are suggestions that seemed crazy, but really work!

For the squash, I wanted to under-bake it by a little, only because I wanted to put it back in the oven with the sauce to finish. For a normal medium-to-large baked spaghetti squash cut like this one, I usually give it about an hour at 350°, so I gave this one 45 minutes.




Freshly Prepared Spaghetti Squash

Spaghetti Squash

Cheese Sauce

Spaghetti Squash

Gooey, Creamy Gluten-Free Mac&Cheese Baked Spaghetti Squash: a warm, comforting, and delectable gluten-free alternative for the holidays! | Tasting Everything


The Most Delectable Healthier Gluten-Free Mac and Cheese Baked Spaghetti Squash

Gooey, Creamy Baked “Mac and Cheese” Spaghetti Squash

Prep Time: 15 minutes

Cook Time: 1 hour, 15 minutes

Gooey, Creamy Baked “Mac and Cheese” Spaghetti Squash


  • 1 medium to large spaghetti squash
  • 1 Tbs olive oil
  • 1 tsp salt
  • 1/2 tsp black pepper
  • For the Mac and Cheese Sauce
  • 1 Tbs butter
  • 1 Tbs flour
  • 1 cup whole milk
  • 1/2 tsp turmeric
  • 1/2 tsp paprika
  • 1/4 tsp mustard powder
  • 1 Tbs sour cream
  • 1/2 cup sharp cheddar cheese, shredded
  • 1/4 cup parmesan cheese, shredded
  • salt and pepper (make sure to use a little more of both than you think you need!)
  • 1 Tbs water
  • To finish:
  • Prepared Squash
  • Mac and Cheese Sauce
  • Salt
  • Pepper
  • 1/2 cup parmesan, shredded or grated
  • 1 bunch chives, chopped


    For the squash:
  • Preheat the oven to 350°
  • Trim both ends off of the squash. Cut it in half lengthwise, coat both sides with olive oil, salt, and pepper. Place the squash cut side down on a piece of parchment paper on a sheet tray.
  • Bake for 45 minutes, remove from the oven, and let cool slightly for 10-20 minutes.
  • Just before pouring the sauce over, use a fork to pull or rake the flesh, separating it into strands. Make sure not to puncture the shell and to leave some flesh still attached all the way around to prevent the sauce from leaking out.
  • For the mac and cheese sauce:
  • In a small saucepan, melt the butter and then whisk in the flour.
  • Stir frequently for 3-5 minutes on a very low heat. You want to have no lumps and smell a kind of gentle, nutty aroma.
  • Add the mustard powder, turmeric, and paprika and stir.
  • Add the milk, and whisk to combine.
  • Stir frequently while the sauce thickens. Let the sauce get fairly thick; you want a sauce that will hold together in the squash halves.
  • Stir in the sour cream and mix well.  
  • Add both cheeses and melt.
  • Season with salt and pepper.
  • At the end, when you have a nice and thick sauce, stir in 1 Tbs water. It will loosen the sauce a little and give it a shiny gloss.
  • To finish:
  • Preheat the oven to 475°
  • Take the squash that you already have prepared and sprinkle it with a little more salt and pepper.
  • Pour the sauce over the squash.
  • Sprinkle the top with the parmesan cheese.
  • Put in the oven for about 15 minutes, or until the top is golden and bubbling.
  • Sprinkle with chives, dig in, and enjoy!


In the mood for more comfort food? You might want to check out the incredibly popular Vegetarian Black Bean Enchiladas with Homemade Red Sauce and Lime Sour Cream!

If you want a light, fresh, and healthy feel-good salad to add to your meal, check out the Citrus and Avocado Salad. Raw, creamy, bright, and so yummy!

Perhaps you are in the mood to check out a different sort of gluten-free baked squash recipe! Here’s Roast Butternut Squash Stuffed with Chorizo and Wild Rice.

Just looking for the gluten-free recipe for warm, dense, and fragrant Sour Cream Best Banana Bread Ever? You might like this one!

There are tons of options available for healthy dinner ideas, healthy salad recipes, and more!

Gooey, Creamy Gluten-Free Mac&Cheese Baked Spaghetti Squash: a warm, comforting, and delectable gluten-free alternative for the holidays! | Tasting Everything

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