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Why settle for boxed mac and cheese when you can have spaghetti squash mac and cheese?! This cheesy-licious dish is a healthier, low-carb twist that still brings all the cozy, comforting flavors. (Bonus: we’ll show you how to serve it in squash bowls with broiled mozza for that perfect gooey, gourmet finish!)

Mac And Cheese 2.0
So, you love mac and cheese but aren’t exactly thrilled about the post-carb coma? (Yeah, I feel you.) Sarah here, putting on my food scientist hat—because I didn’t spend years studying nutrition just to let these delicious cheesy noodles get the better of me.
Enter spaghetti squash mac and cheese, the low-carb solution to everyone’s favorite comfort food! For the uninitiated, spaghetti squash is a yellow squash that, when cooked, transforms into strands of “spaghetti” (it’s like magic!).
Reader rating
“I loved your cauliflower mac and cheese, so I had to try this. It is great, but the best part is serving it in the shells. It came out as artistic looking as your photos. I had a couple of friends and it was a huge hit. Thanks, Sarah!” —GW

Here’s What You’ll Need
Grab your squash and a few pantry staples, and let’s create your new favorite meal!
- Spaghetti Squash: One spaghetti squash provides two large servings. (Consider doubling the recipe for a crowd of four.)
- Olive Oil: Aids in the roasting process, helping the squash reach a perfect golden hue. Use extra-virgin olive oil if possible!
- Milk: We’ll be making a classic cheese sauce, so we’ll need some milk (regular or dairy-free) to form the base.
- Roux: A pat of unsalted butter will bind with all-purpose flour to form a roux, thickening our cheese sauce into dreamy cheesiness. Feel free to use a gluten-free all-purpose flour to keep the dish free of gluten!
- Cheese: Mac and cheese isn’t complete without cheese! Use 2 cups of shredded sharp cheddar, or if you’re up for a different flavor, try Gouda, Gruyère, or Fontina! (Optionally, top it with mozzarella for broiling.)
- Mustard: Cuts through the richness of the cheese, adding a much-needed zing. The flavor is undetectable, but you’ll love what it does for the dish!
- Seasonings: A pinch of salt, pepper, and garlic powder adds extra flavor.

Ready in 4 steps
Spaghetti squash recipes often get a rep for being difficult or time-consuming, but that is so not the case here! This spaghetti squash mac and cheese takes 45 minutes in total (and is worth every second).
Step 1: Roast The Squash
Cut the squash and scoop out the seeds. Drizzle and rub the inside with oil, then roast the squash until fork tender but still a little firm. When finished, flip the squash over and allow it to cool enough to touch.

Step 2: Prepare the Sauce
Warm the milk in the microwave, then melt the butter over medium heat in a large sauté pan. Whisk in the flour to form a smooth paste (your roux). Slowly drizzle in the milk, whisking constantly until it’s fully incorporated. Lastly, stir in the cheese, mustard, and seasonings.

Step 3: Spaghettify The Squash
Use a fork to scrape strands from the inside of the spaghetti squash.

Step 4: Add The Strands
Transfer the spaghetti strands to the pan with the sauce. You can serve your spaghetti squash mac and cheese now or move on to Step 5 if you’d like to double-bake it for extra cheesiness!

Step 5: Optional Double Bake
Spoon the mac and cheese mixture back into the spaghetti squash shells and top with shredded mozzarella cheese. Set in the oven and broil for 2 to 3 minutes, watching closely until the cheese melts and turns golden brown.

Complete Your Meal
Now that we’ve created the dreamiest bowls of squashy cheesiness, we need some greens! Here are a few veggie-loaded sides that pair well with this spaghetti squash mac and cheese.
- Roasted Asparagus with Romesco Sauce: This dish is perfect for lightening up your bowls with a pop of green and some zesty sauce.
- Zucchini Corn Salad: What could be more fitting than pairing squash with more squash?
- Fresh Veggie Lettuce Wraps: The crispness of the lettuce balances the richness of this cheesy masterpiece.


Spaghetti Squash Mac ‘n Cheese (Low Carb)
Ingredients
- 1 spaghetti squash
- 1 Tbsp olive oil, 15 mL
- 1 cup milk, low fat or 2%, 236 mL
- 2 Tbsp unsalted butter, 28 g
- 2 Tbsp all-purpose flour, 20 g
- 2 cups shredded sharp cheddar cheese, 225 g
- ½ tsp mustard
- ¼ tsp each salt, pepper, garlic powder
- Optional: ½ cup shredded mozzarella, 50 g
Instructions
- Prep: Preheat oven to 400°F (204°C). Cut spaghetti squash in half* and scoop out the seeds. Drizzle the inside with olive oil, rubbing to coat evenly. Place cut-side down on a baking sheet and prick the outside with a fork. Roast for about 30 minutes until fork tender but still a little firm. When finished, flip over and allow to cool enough to the touch.
- Sauce: While squash cooks, heat milk in the microwave until lukewarm, about 30 seconds. Melt butter over medium heat in a large saute pan. Whisk in flour to form a smooth paste. Slowly drizzle in the milk, whisking constantly until it's fully incorporated. Increase heat and cook while whisking until the mixture thickens into a thick sauce. Stir in cheese, mustard, salt, pepper, and garlic powder. Remove from heat and cover to keep warm.
- Spaghettify: Use a fork to scrape strands from the inside of the spaghetti squash (if serving in the squash shell, leave about ¼ inch of flesh in the squash to support your bowls).
- Assemble: Transfer spaghetti strands to your pan with the sauce, stirring to combine. You can eat it at this point, or double-bake it.
- Optional Double Bake: Optionally, spoon the mac and cheese mixture back into the spaghetti squash shells and top with mozzarella cheese. Set in the oven and broil for 2 to 3 minutes, watching closely until cheese melts and turns golden brown.
Notes
Nutrition
Nutrition information calculated by Sarah Bond, degreed nutritionist.

















I loved your cauliflower Mac and Cheese, so I had to try this. It is great, but the best part is serving it in she shells. It came out as artistic looking as your photos. I had a couple of friends and it was a huge hit. Thanks Sarah
Aw yay! So awesome to hear! Enjoy! 😀
This was very good but used half the cheese as it would’ve been too much with 2 cups…still needed pasta …used gluten free and nutmeg, cayenne to help with seasoning.
Made this last night! Surprisingly easy, and it was great! I’ve decided to go vegetarian, and this was my first recipe under my new program – I downloaded the week of fall recipes. Thank you for all your wonderful cooking support!
I would add a little more flavor to the mac & cheese next time – probably smoked paprika.
I’m so happy you liked it, Lisa! Smoked paprika sounds like such a tasty addition! 😀
Can I use a plant based milk!
Yep that should work! 🙂
I made this recipe yesterday and it was SOOOOO GOOD!!! I would have taken a picture to share, but it didn’t come out nearly as pretty as it was delicious!
I’m so thrilled to hear it was a hit, Danielle! Happy eating!