Butternut Squash Mac and Cheese with Cottage Cheese

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

• Naturally creamy: Cottage cheese and roasted butternut squash create a smooth, rich sauce without heavy cream.
• Balanced flavor: Mild seasonings showcase the squash and cheese, making the dish appealing for both children and adults.
• Wholesome ingredients: Made with gluten-free pasta, almond milk, and fresh cheeses for a nourishing meal.
• Crispy topping: A buttery almond flour crumble adds crunch and a golden finish.

Ingredients & Substitutions

Everything you need to make this cottage cheese mac and cheese with roasted butternut squash

Pasta: Choose any gluten-free pasta you prefer — brown rice, quinoa, chickpea, or other gluten-free noodles work well.

Roasted Butternut Squash: If fresh squash isn’t available, use canned or frozen puree as a substitute.

Light Olive Oil: Vegetable, canola, or coconut oil can be used in its place.

Onion: Shallots or red onion are good alternatives to white onion.

Garlic: Garlic powder or paste can replace fresh minced garlic if needed.

Cottage Cheese: For a different texture, substitute with ricotta, sour cream, or additional milk.

Vegetable Stock: Chicken or beef broth are acceptable swaps; vegetable bouillon dissolved in water also works.

Butter: Use dairy-free margarine or vegan butter for a lactose-free option.

Almond Flour: Swap with gluten-free all-purpose flour or rice flour in the roux. For the crumble, gluten-free breadcrumbs or crushed crackers can replace almond flour.

Almond Milk: Any unsweetened non-dairy milk — soy, oat, or coconut — may be used instead.

Cheddar Cheese: Mix in other meltable cheeses like gouda, Monterey Jack, or white cheddar for a customized flavor. Avoid pre-shredded cheese if you want a truly smooth melt.

Parmesan Cheese: Use a vegan Parmesan alternative or nutritional yeast to add a savory note without dairy.

Paprika: Smoked paprika, chili powder, or a pinch of cayenne will alter the flavor profile; add spices gradually and taste as you go.

Step 1: Roast the Butternut Squash

Preheat the oven to 400°F (204°C). Trim the ends of the squash, then cut it in half lengthwise. Scoop out and discard the seeds.

Line a baking sheet with parchment paper. Brush or spray the cut sides lightly with olive oil and season with salt and pepper. Place the halves cut-side down and roast for about 1 hour, until very tender.

Let cool slightly, then scoop the flesh into a bowl and discard the skins. The roasted squash can be prepared ahead and stored in the refrigerator in an airtight container for a day or two.

Step 2: Prep the Ingredients

Preheat the oven to 375°F (190°C). Cook the pasta according to package directions until al dente, then drain and set aside.

Shred the cheese, finely mince the garlic, and roughly chop the onion. Measure out the rest of the ingredients so assembly is smooth and efficient.

Step 3: Make the Sauce

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

Transfer the sautéed onion and garlic to a blender. Add the roasted butternut squash, cottage cheese, vegetable stock, salt, and paprika. Blend until completely smooth, then set the puree aside.

Step 4: Make the Roux and Finish the Sauce

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

Gradually whisk in 1 cup almond milk, cooking and stirring until the mixture thickens, about 2–3 minutes. Add the blended butternut squash mixture and heat through until smooth.

Remove from heat and stir in 2 cups shredded cheddar cheese until fully melted and integrated into the sauce. Adjust seasoning to taste.

Step 5: Make the Crumble

In a small bowl combine 3 tablespoons melted butter, 1/2 cup almond flour, 1/4 teaspoon salt, 1/2 teaspoon paprika, 1/2 teaspoon garlic powder, and 1/2 cup grated Parmesan. Mix with a fork until the texture is crumbly.

Step 6: Assemble and Bake

Grease a 9×13-inch baking dish and transfer the cooked pasta into it. Pour the butternut squash cheese sauce over the pasta and gently fold to combine.

Evenly sprinkle the crumble topping over the pasta and bake at 375°F for 25–30 minutes, until the top turns golden and the edges are bubbling.

Allow the casserole to rest a few minutes before serving so it sets slightly for easier portioning.

Gluten-Free Macaroni and Cheese Recipe Notes

Butternut Squash: Roasting concentrates the squash’s flavor and caramelizes the natural sugars. If you prefer, peel and dice, then boil until tender, or use frozen squash as a time-saving option.

Pasta Choice: Cook gluten-free pasta to al dente since it will finish cooking in the oven. Different brands vary in texture; choose one you like.

Sauce Consistency: Thin with additional vegetable stock or almond milk if too thick. If too thin, simmer gently to reduce and thicken. A high-speed blender gives the smoothest texture, though an immersion blender will work with slightly less silkiness.

Baking Time: Watch the casserole while it bakes to avoid over-browning. Cover with foil if the topping browns too quickly.

Serving Suggestions

This mac and cheese works well as a side or main. Add cooked bacon, pulled pork, diced chicken, or steak for extra protein. Finish with fresh herbs such as chives, parsley, or thyme for brightness.

Cottage Cheese Mac and Cheese with Butternut Squash