Spaghetti Squash Mac and Cheese (Paleo, Whole30, Keto)

Spaghetti Squash Mac and Cheese bring together all the flavors of traditional macaroni and cheese in a wholesome gluten and dairy free recipe. Spaghetti squash is baked in a velvety cashew cream sauce with hints of cracked nutmeg. This Whole30 compatible and keto friendly dish is the perfect dinner side but is also filling enough to be a main dish.

Spaghetti Squash Mac and Cheese

Spaghetti squash mac and cheese is tender roasted spaghetti squash tossed in a luscious, creamy, “cheesy” sauce for a healthier alternative to traditional macaroni and cheese. Recently my daughter asked me to make my Classic Macaroni and Cheese for dinner. The smell of the mac and cheese baking made me long for a bite but I was finishing up a round of Whole30.

So I pulled together a Whole30 friendly mac and cheese substitute with ingredients I had on hand. I shared the process on Instagram and everyone loved it. This easy spaghetti squash mac and cheese was so unbelievably delicious and wholesome that I just had to share the recipe here!

Why You’ll Love This Spaghetti Squash Mac and Cheese Recipe

• Healthy Alternative: If you love the cheesy, carby goodness that is classic mac and cheese but needs something low carb, keto friendly, and Whole30 Compliant, this is the answer!
• So Easy to Make: Roast the squash, make your sauce, combine, and bake. It’s really that simple!
• Absolutely Delicious: Satisfy your cheesy pasta craving because this is nutritious comfort food!

What is Spaghetti Squash?

Spaghetti squash is nature’s spaghetti and a great substitute for pasta dishes if you’re gluten free or on a low carb diet. This squash is low in calories, nutrient dense and linked to many health benefits. To read more about this vibrant vegetable click here.

I first learned about spaghetti squash when I was working at a marketing agency in New York City. One of my coworkers pulled a bowl of spaghetti squash from the microwave, while I was waiting for a turn to reheat my lunch. As an immigrant, living with my parents I mostly ate what my mother cooked and she was certainly not cooking this. Over the years I’ve cooked my fair share of spaghetti squash and it is now part of my regular diet.

Ingredients for Spaghetti Squash Mac and Cheese

You’ll be amazed at how this list of ingredients comes together to create a delicious “pasta” dish!

For the Spaghetti Squash:

• Spaghetti squash: Use a squash that is about 3 lbs. Be mindful that cooking time has o be adjusted if using a smaller or larger squash.
• Olive oil: This helps the salt stick to the surface of the squash.
• Kosher salt: To taste.

For the Cashew Cream:

• Raw cashews: The main ingredient is a rich, creamy base when soaked.
• Warm water: The liquid helps the sauce blend easily.
• Cloves of garlic: Alternatively, use 1 teaspoon of garlic powder.
• Nutritional yeast: This adds a bit of “cheesy flavor” and mimics the taste of cheese. It gives it the right hint of cheesiness and almost tricks your brain into thinking that there is actually cheese in this dish.
• Yellow onion: Alternatively, use 1 tbsp of onion powder.
• Table salt: To taste.

Other Ingredients:

• Parsley flakes: or 1 tbsp of freshly chopped parsley
• Eggs: This binds the sauce and spaghetti.
• Spicy brown mustard: Add this for a warm, zesty spiced quality.
• Spices: I use freshly grated nutmeg (optional) and smoked paprika (used as garnish).
• Nutritional yeast: Used as a garnish for a cheesy tasting finish.

See recipe card for quantities.

Why Use Nutritional Yeast?

Nutritional yeast is a yeast species that is “grown specifically to be used as a food product. The yeast cells are killed during manufacturing and not alive in the final product. It is used in cooking and has a cheesy, nutty or savory flavor. It is a great source of B vitamins, protein and other trace minerals. Learn more about nutritional yeast from this Healthline.com article.

How to Make Spaghetti Squash Mac and Cheese

Cooking Spaghetti Squash

To roast the squash in the oven:

Start by cutting the squash in half length wise, then scooping out the guts (stringy bits inside) and seeds.

Drizzle with olive oil and salt.

Place squash cut side down on a sheet pan and bake at 350°F for 30-40 minutes, depending on the size of your squash, or until a fork can easily pierce the exterior.

Remove from the oven and using a fork shred the flesh of the squash until it separates into spaghetti-like pieces

Make the Cashew Cream

The cashew cream is what makes this dish truly a winner. It is so easy to make. Raw cashews blended with pantry staples in a quick, less than 5 minutes process. Some people like to soak the cashews for an hour or two. I’ve done it both ways in my smoothie blender cup and the results were the same. Easy “cheesiness” without the work or the tummy ache from dairy!

Pulling the dish together

The hardest part of this recipe is cutting open the spaghetti squash! Once you get through that step it’s smooth sailing. If you have an instant pot and steam your squash in there, that saves you on about 30 minutes of prep time. Everything else is pretty much dump, mix, bake and enjoy! I hope you give this baked spaghetti squash mac and cheese recipe a try because it’s my new favorite side dish!

Substitutions & Variations for Spaghetti Squash Mac and Cheese

• Vegan Spaghetti Squash Mac and Cheese. Simply omit the egg to make this recipe vegan.
• Instant Pot Spaghetti Squash Mac and Cheese. My preferred method of cooking spaghetti squash is to roast it in the oven, but there are also recipes with instructions for cooking it in the instant pot. Like this one! I haven’t tried this yet (not sure why) but it looks quick and easy which is right up my alley.
• Dairy. If you enjoy milk and cheese as part of your diet, you can use real cheese sauce. Swap the creamy cashew sauce and nutritional yeast for shredded cheese, butter, and milk. I suggest mozzarella cheese, parmesan cheese, swiss cheese, or cheddar cheese but use whatever cheese your taste buds desire! Please not that adding dairy would no longer make this recipe Whole30 or Paleo Compatible.
• More Add-Ins. For a salty savory addition, mix in cooked bacon bits. Want a delectable crispy topping? This recipe is also great with some sautéed chicken added in before baking. For more nutrients, add cooked broccoli (pulsed in a food processor for about 10 seconds), spinach, or green peas.

Equipment

• Individual Ramekins: For baking 4-6 depending on the size or a casserole baking dish.
• Sheet pan, baking sheet, or cookie sheet: Use this to roast the spaghetti squash.
• Blender or smoothie blender cup: Use this to blend the cashew cream sauce.
• Large Bowl: This contains the shredded spaghetti squash for mixing.

Storage

Store leftovers in an airtight container in the fridge for up to 5 days. For longer storage freeze for up to 1 month. Reheat on the stove over medium-low heat until warmed through. You may need to add vegetable or chicken broth to thin out the sauce if it’s too thick.

Frequently Asked Questions