Cottage Cheese Mac and Cheese Butternut Squash

Make my creamy, healthier spin on Cottage Cheese Mac and Cheese with roasted butternut squash, almond milk, almond flour, onions, garlic, fresh cheese, and your favorite gluten-free pasta. It has a delicious almond flour and butter crumble on top. Adults and kids will love this recipe because the nutrient-dense ingredients are hidden in a rich, cheesy sauce!

Pan of Mac and Cheese Gluten-Free with Roasted Butternut Squash.

Make my Baked Gluten-Free Cottage Cheese Mac and Cheese with Butternut Squash recipe with a sophisticated flavor that adults will love and a classic cheesiness that kids will devour. I’m giving a healthier spin on this classic comfort food with roasted butternut squash, cottage cheese, almond milk, almond flour, onions, garlic, fresh cheese, and your favorite gluten-free pasta. It has a delicious almond flour and butter crumble on top and is perfectly seasoned for mild flavor. 

YouTube video

Why You’ll Love This Butternut Squash Macaroni and Cheese Recipe

  • You only need a few simple ingredients.
  • It is super easy to make for an impressive result.
  • The flavor-rich ingredients make it taste amazing!
  • All the ingredients are easily digestible for a gentle tummy.
Plate of Mac and Cheese Gluten-Free with Roasted Butternut Squash.

Ingredients & Substitutions

Here is everything you need to make the best-tasting cottage cheese mac and cheese with butternut squash:

Pasta: Use gluten-free pasta of your choice, such as brown rice pasta, whole wheat macaroni, quinoa pasta, chickpea pasta or gluten-free noodles.

Roasted Butternut Squash: You can substitute with canned or frozen butternut squash puree if you don’t have fresh roasted squash.

Light Olive Oil: Substitute with vegetable oil, canola oil, or coconut oil.

Onion: Use shallots or red onion as a replacement for white onion.

Garlic: Garlic powder or garlic paste can be used instead of minced garlic.

Cottage Cheese: Replace cottage cheese with sour cream, ricotta cheese, or additional milk.

Vegetable Stock: Swap vegetable stock with chicken or beef broth, or use a vegetable bouillon cube dissolved in water.

Butter: Use a dairy-free margarine or vegan butter if you need a dairy-free option.

Almond Flour: Almond flour can be substituted with gluten-free all-purpose flour or rice flour in the roux. Almond flour is also used in the crumble. You can replace it with gluten-free bread crumbs or crackers.

Almond Milk: Replace almond milk with any other non-dairy milk like soy milk, oat milk, or coconut milk.

Cheddar Cheese: You can use any variety of block cheese that can be grated and melted, including gouda cheese, Monterey jack, and white cheddar. You can use multiple kinds of cheese to customize the flavor. I do not recommend pre-shredded cheese because it has been coated in cellulose and won’t melt down as smooth and creamy.

Parmesan Cheese: Swap grated Parmesan cheese with a dairy-free or vegan Parmesan cheese alternative, or use nutritional yeast for a cheesy flavor.

Paprika: You can replace paprika with smoked paprika, chili powder, or cayenne pepper for a different flavor. Go easy on the spices and be sure to taste as you go.

Mac and Cheese Gluten-Free with Roasted Butternut Squash

How to Make My Cottage Cheese Mac and Cheese Gluten-Free with Roasted Butternut Squash

Step 1: Roast the Butternut Squash

Preheat your oven to 400°F. Place your butternut squash on a cutting board and carefully cut off the bottom and the top of the squash. Begin by pressing your knife into the skin about 1/2″ and work your way around the end of the squash. When you get back to your starting point, push your knife deeper into the squash and cut off the end.

Then, place your squash upright and carefully slice it in half down the middle. Keep both hands on top of the knife and gently rock it back and forth as you press it down through the squash.

Scoop out the seeds with a large spoon. 

Adding wet ingredients to muffin batter.
Mixing cranberries into muffin batter.

Scoop out the seeds with a large spoon. 

Adding wet ingredients to muffin batter.
Mixing cranberries into muffin batter.

Line a baking sheet with parchment paper for easy clean-up. Lay the squash in the pan, cut side up, and brush or spray with a bit of olive oil. Then sprinkle with a dash of salt and pepper. Flip them over so they are cut side down on the sheet. Bake at 400°F for 1 hour. Remove the pan from the oven and allow to cool.

Adding wet ingredients to muffin batter.
Mixing cranberries into muffin batter.

Scrape out the soft roasted butternut squash, set it aside in a bowl, and discard the skins. This step is best done a few hours before making the soup or even a day or two in advance. Store the squash in an air-tight container in the fridge until needed.

Adding wet ingredients to muffin batter.
Mixing cranberries into muffin batter.

Step 2: Prep the Ingredients

Preheat your oven to 375°F.

Cook the pasta according to the package directions until it’s al dente. Drain and set aside.

Shred 3 packed cups of cheese. Finely dice 4 cloves of garlic. Roughly chop 1/2 onion. 

Step 3: Make the Sauce

In a large saucepan, heat 1 tablespoon of light olive oil over medium-high heat. Add the diced onion and minced garlic. Sauté for about 5 minutes, or until the onion is soft and translucent.

In a high-speed blender or food processor, combine the roasted butternut squash, sautéed onion and garlic, cottage cheese, vegetable stock, salt, and paprika. Blend until smooth and set aside.

Sauteeing onions and garlic in pot.
Ingredients combined in blender for cheese sauce.

Step 4: Make the Roux

In the same saucepan, melt 2 tablespoons of butter over medium heat. Stir in 1/4 cup of almond flour and cook for 1-2 minutes to create a roux.

Gradually whisk in 1 cup of almond milk, and continue to cook and stir until the mixture thickens, about 2-3 minutes.

Add the butternut squash puree from the blender into the saucepan, and stir to combine. Cook for another 2-3 minutes, or until the sauce is smooth and heated through.

Pour in the butternut squash mixture and stir until well combined. 

Remove the saucepan from heat and stir in 2 cups of shredded cheddar cheese until it’s melted and the sauce is well combined with the cheese.

Adding almond milk to rouxe in pot.
Stirring together rouxe and cheese sauce in a pot.

Step 5: Make the Crumble

In a separate bowl, prepare the crumble topping by combining 3 tablespoons of melted butter, 1/2 cup of almond flour, 1/4 teaspoon of salt, 1/2 teaspoon of paprika, and 1/2 teaspoon of garlic powder and 1/2 cup parmesan cheese. Use a fork to mix the ingredients until they form a crumbly texture.

Step 6: Assemble the Dish

Transfer the pasta to a greased 9×13-inch baking dish. Pour the sauce over the pasta and gently mix it in until well combined.

Sprinkle the prepared crumble topping evenly over the pasta and sauce.

Bake the mac and cheese in the preheated oven for about 25-30 minutes, or until the top is golden brown and the edges are bubbling.

Once done, remove it from the oven and let it cool for a few minutes before serving.

Stirring cheese sauce and pasta in baking dish.
Sprinkling crumble on mac and cheese.
Pan of Mac and Cheese Gluten-Free with Roasted Butternut Squash.

Gluten-Free Macaroni and Cheese Recipe Notes

Butternut Squash: Roasting your butternut squash will result in the best flavor. But you can also peel and dice your butternut squash and then boil until soft. Or you can use frozen which is already soft.

Pasta Choice: Use your preferred gluten-free pasta and cook it to al dente, as it will continue to cook while baking.

Sauce Consistency: If your sauce seems too thick, you can thin it with a little more vegetable stock or almond milk. Conversely, if it’s too thin, you can simmer it a bit longer to thicken. You can blend the sauce with an immersion blender but it will not be as smooth as using a high speed blender.

Baking Time: Keep an eye on the dish while baking to prevent over-browning.

Serving Suggestions:

Works as a side for almost any meal. Add crumbled bacon, pulled pork or diced chicken or steak for extra protein. Top with a sprinkle of herbs like chives, parsley or thyme for freshness.

Refrigeration: If you have leftovers or want to store the dish before serving, allow it to cool to room temperature. Cover the baking dish with plastic wrap or aluminum foil or transfer the mac and cheese to an airtight container.

Shelf Life: Stored properly in the refrigerator, your mac and cheese should remain safe to eat for up to 5-7 days.

Reheating: When you’re ready to reheat, you can do so in the microwave or the oven. Reheat in the microwave in 1-2 minute intervals, stirring in between until it’s hot throughout. If using the oven, cover the dish with foil to prevent further browning and bake at a lower temperature, around 325°F (163°C), until heated through.

Freezing: If you want to freeze your mac and cheese, it’s best to do so before baking. Assemble the dish, but don’t add the crumble topping. Wrap it tightly in a double layer of plastic wrap and aluminum foil. Properly stored in the freezer, it can last for 2-3 months.

Thawing and Baking from Frozen:

To use the frozen mac and cheese, thaw it in the refrigerator overnight. Once thawed, add the crumble topping and bake according to the original recipe instructions.

Is macaroni and cheese gluten-free?

Yes, when you use gluten free pasta and almond flour for the roux.

Do you have to use gluten-free pasta for this recipe?

No, you can use your preferred pasta.

What can I substitute for roasted butternut squash?

If you don’t have roasted butternut squash, you can use canned or frozen butternut squash puree as an alternative.

Can I prepare this dish in advance?

Yes, you can assemble the mac and cheese in advance and refrigerate it before baking. Just add the crumble topping right before baking.

Can I freeze this mac and cheese?

Yes, you can freeze this dish, but it’s best to do so before baking. Assemble the mac and cheese without the crumble topping, wrap it tightly, and store it in the freezer. Thaw it in the refrigerator before adding the crumble topping and baking.

How do I prevent the crumble topping from becoming too brown during baking?

If the crumble topping is browning too quickly, you can cover the dish with foil during the last part of the baking time to prevent over-browning.

Here are some more cozy gluten-free recipes:

Cottage Cheese Mac and Cheese Butternut Squash Recipe

Gluten-Free diet-friendly recipe
Make my creamy, healthier spin on Cottage Cheese Mac and Cheese with roasted butternut squash, almond milk, almond flour, onions, garlic, fresh cheese, and your favorite gluten-free pasta. It has a delicious almond flour and butter crumble on top. Adults and kids will love this recipe because the nutrient-dense ingredients are hidden in a rich, cheesy sauce!
5 from 2 votes
Servings 16
Prep Time 45 minutes
Cook Time 30 minutes
Total Time 1 hour 15 minutes

Ingredients
  

  • 1 pound dried pasta of choice

Sauce:

  • 4 cups roasted butternut squash
  • 1 tablespoon light olive oil
  • 1/2 onion diced
  • 4 cloves garlic minced
  • 1 cup cottage cheese
  • 1 cup vegetable stock
  • 2 teaspoons salt
  • 2 teaspoons paprika
  • 2 tablespoons butter
  • 1/4 cup almond flour
  • 2/3 cup almond milk
  • 2 cups cheddar cheese shredded

Crumble:

  • 3 tablespoons butter
  • 1/2 cup almond flour
  • 1/4 teaspoon salt
  • 1/2 teaspoon paprika
  • 1/2 teaspoon garlic powder
  • 1/2 cup parmesan cheese grated

Instructions
 

Roast the Butternut Squash:

  • Preheat your oven to 400°F. Place your butternut squash on a cutting board and carefully cut off the bottom and the top of the squash. Begin by pressing your knife into the skin about 1/2" and work your way around the end of the squash. When you get back to your starting point, push your knife deeper into the squash and cut off the end.
    Then, place your squash upright and carefully slice it in half down the middle. Keep both hands on top of the knife and gently rock it back and forth as you press it down through the squash. Scoop out the seeds with a large spoon. 
    Line a baking sheet with parchment paper for easy clean-up. Lay the squash in the pan, cut side up, and brush or spray with a bit of olive oil. Then sprinkle with a dash of salt and pepper. Flip them over so they are cut side down on the sheet. Bake at 400°F for 1 hour. Remove the pan from the oven and allow to cool.
    Scrape out the soft roasted butternut squash, set it aside in a bowl, and discard the skins. This step is best done a few hours before making the soup or even a day or two in advance. Store the squash in an air-tight container in the fridge until needed.

Mac and Cheese:

  • Preheat your oven to 375°F.
    Cook the pasta according to the package directions until it's al dente. Drain and set aside.
    Shred 3 packed cups of cheese. Finely dice 4 cloves of garlic. Roughly chop 1/2 onion. 
  • In a large saucepan, heat 1 tablespoon of light olive oil over medium-high heat. Add the diced onion and minced garlic. Sauté for about 5 minutes, or until the onion is soft and translucent.
    In a high-speed blender or food processor, combine the roasted butternut squash, sautéed onion and garlic, cottage cheese, vegetable stock, salt, and paprika. Blend until smooth and set aside.
  • In the same saucepan, melt 2 tablespoons of butter over medium heat. Stir in 1/4 cup of almond flour and cook for 1-2 minutes to create a roux.
    Gradually whisk in 1 cup of almond milk, and continue to cook and stir until the mixture thickens, about 2-3 minutes.
    Add the butternut squash puree from the blender into the saucepan, and stir to combine. Cook for another 2-3 minutes, or until the sauce is smooth and heated through.
    Pour in the butternut squash mixture and stir until well combined. 
    Remove the saucepan from heat and stir in 2 cups of shredded cheddar cheese until it's melted and the sauce is well combined with the cheese.
  • In a separate bowl, prepare the crumble topping by combining 3 tablespoons of melted butter, 1/2 cup of almond flour, 1/4 teaspoon of salt, 1/2 teaspoon of paprika, and 1/2 teaspoon of garlic powder and 1/2 cup parmesan cheese. Use a fork to mix the ingredients until they form a crumbly texture.
  • Transfer the pasta to a greased 9×13-inch baking dish. Pour the sauce over the pasta and gently mix it in until well combined.
    Sprinkle the prepared crumble topping evenly over the pasta and sauce.
    Bake the mac and cheese in the preheated oven for about 25-30 minutes, or until the top is golden brown and the edges are bubbling.
    Once done, remove it from the oven and let it cool for a few minutes before serving. 

Video

YouTube video

Notes

Butternut Squash: Roasting your butternut squash will result in the best flavor. But you can also peel and dice your butternut squash and then boil until soft. Or you can use frozen which is already soft.
Pasta Choice: Use your preferred gluten-free pasta and cook it to al dente, as it will continue to cook later while baking.
Sauce Consistency: If your sauce seems too thick, you can thin it with a little more vegetable stock or almond milk. Conversely, if it’s too thin, you can simmer it a bit longer to thicken. You can blend the sauce with an immersion blender but it will not be as smooth as using a high speed blender.
Baking Time: Keep an eye on the dish while baking to prevent over-browning.

Nutrition

Calories: 311kcalCarbohydrates: 30gProtein: 12gFat: 17gSaturated Fat: 6gPolyunsaturated Fat: 1gMonounsaturated Fat: 3gTrans Fat: 0.1gCholesterol: 28mgSodium: 615mgPotassium: 231mgFiber: 3gSugar: 3gVitamin A: 4199IUVitamin C: 8mgCalcium: 210mgIron: 1mg
Keyword casserole, mac and cheese, macaroni
Did you make this recipe?Please let me know in the comments below how it turned out 🙂
5 from 2 votes (2 ratings without comment)

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