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Spaghetti Squash Mac and Cheese is a lower-carb version of Mac and cheese, and so unbelievable tasty. Roast the spaghetti squash to al dente, make a quick roux, and then add in cheddar cheese, parmesan cheese, frozen peas, and bacon. So delicious!

We also love the REAL Mac and Cheese too. For a “smoky” version, try my Smoked Pimento Mac and Cheese, created by my oldest son! Or my Quick and Easy Mac and Cheese is great for a simpler version.

Side view of spaghetti squash casserole with bacon on top.

Healthy Spaghetti Squash Recipe

I love my pasta and bread, but over the years, I’ve cut back on those food groups dramatically. I still enjoy a great baked shells dish or pasta salad, but I’m always searching for lower-carb pasta dishes too. This one is an oldie, and I’m reviving it from the very early blog days. It’s about time, because it’s really too good to ignore!

If you are wondering if it tastes like Mac and cheese, I’d say no. But if you like spaghetti squash, cheese, and bacon, you’re gonna love this one. And if you’ve never tried spaghetti squash, this would be an excellent first for you. The flavors are perfect together, and I think you’ll love it like we do. 😀

By the way, I DO have some healthier recipes that include actual pasta too, like my Skinny Fettuccini Alfredo and my Rigatoni Pasta with Sausage and Broccoli. I also love using butternut squash as a pasta sauce and use it in my Butternut Squash Lasagna with Spinach and my Creamy Butternut Squash Pasta.

Side shot of a casserole with a spoonful of spaghetti squash.

Ingredients needed for Spaghetti Squash and Cheese

Spaghetti Squash – You’ll need two medium spaghetti squash, or about 7 cups after roasting.
Olive Oil, Kosher Salt and Freshly Ground Black Pepper – For drizzling on the squash.
Roux Ingredients – Use onion, garlic, flour, chicken broth, milk, kosher salt, freshly ground black pepper, and red pepper flakes.
Cheese – Use freshly grated cheddar cheese and parmesan cheese. I recommend staying away from the pre-shredded cheese because they don’t melt as well.
Add-In Ingredients – Cooked and crumbled bacon and frozen peas.

Sliced spaghetti squash ready to bake. — before baking the squash

The baked spaghetti squash. — before baking the squash

Bowls of the shredded cheese. — the cheddar cheese and parmesan cheese

A bowl for the frozen peas and the cooked bacon. — the cheddar cheese and parmesan cheese

How to make Spaghetti Squash Mac and Cheese

Roast the spaghetti squash. Begin my microwaving your spaghetti squash slightly to soften them so slicing is easier (and safer). I usually microwave each squash for about two to three minutes and then cool slightly. Slice the spaghetti squash width-wise in round sections. Remove the seeds, and place on a prepared baking sheet. Roast in the oven until al dente. “Comb” the spaghetti squash from the skins, and set on paper towel to soak up some of the liquid.
Cook the bacon. After the spaghetti squash cooks, place bacon on a wire rack on a baking sheet, and cook until crispy. Remove to cool. (Or you can cook it in the microwave as an alternative).
Make the roux. In a large stock pan, combine chopped onion with olive oil and butter. Cook over medium-high heat until soft, add garlic, and stir for 30 seconds. Add seasonings, and then flour. Cook for a couple of minutes, and then add chicken broth and milk. Reduce heat and cook until the mixture thickens, about 5-6 minutes.
Add cheese. Add the shredded cheddar and parmesan cheese, and stir until melted.
Add the additional ingredients. Add the frozen peas and cooked and crumbled bacon. Then add the cooked spaghetti squash and stir well.
Bake. Pour mixture into a baking dish, and bake for approximately 30 minutes.
EAT.

A stock pot of the roux with the other ingredients on top. — the roux

Overhead view of the baked spaghetti squash recipe.

Frequently Asked Questions

What is spaghetti squash? Spaghetti squash is a variety of winter squash with slightly stringy flesh that when cooked resembles spaghetti. It doesn’t actually taste like pasta, but it is a great alternative when mixing it with sauces and different spices.
Is spaghetti squash healthy? Spaghetti squash is low in calories and high in fiber, making it a healthy option. One cup has only 31 calories, far less than a cup of pasta noodles, and has 2 grams of fiber. This squash is also a good source of calcium, potassium, magnesium, and niacin.
Can you overcook spaghetti squash? YES. I’ve done it, and it’s mushy and lacks flavor. Be careful to cook it to AL DENTE, leaving a little bite as you would with regular pasta. Test it with a fork as it roasts in the oven.

How to Cook Spaghetti Squash

There are lots of ways to cook spaghetti squash on the internet. All you have to do is to google it and you’ll have plenty of choices. Here are a few and btw, #3 is my favorite.

Cook in the microwave. You can always use the microwave to cook the squash. I’ve seen people who recommend cooking it whole or slicing it in half. I’ve never personally done it this way.
Use the instant pot. Here is the way I’ve done it. Cut the squash in fourths, remove seeds, add one cup of water to the pot, and lay the squash on a trivet inside the pot. Pressure cook for 9 minutes.
Roast in the oven. This is the method I normally choose. I start by softening it (slightly) in the microwave so it’s easier to slice. Then I slice it in rings, drizzle with olive oil, add salt and pepper, and roast until al dente. (Don’t overcook it!) I find that the flavor is the best with this method, but any of these work fine.

A wooden spoon lifting up some spaghetti squash Mac and cheese.

Kitchen Tools Used: (affiliate links)

xoxo ~Sue