When I first made these Butternut Squash Mac & Cheese Cups, I didn’t expect them to become such a staple in my kitchen. I remember hosting a cozy fall gathering where I wanted something familiar yet unique to serve.

Traditional mac and cheese felt a little too heavy, so I decided to experiment with creamy roasted butternut squash. The result? A golden, velvety cheese sauce with just the right balance of sweetness and richness, baked into adorable handheld cups that disappeared from the table in minutes.

What I love most is how versatile they are—you can pack them into lunchboxes, serve them as appetizers at parties, or keep them as a comforting snack for chilly evenings.

Every bite delivers that nostalgic mac-and-cheese comfort with a wholesome twist, thanks to the squash. Honestly, these little cups feel like the perfect marriage of comfort food and nutrition.

Why You’ll Love This Recipe

Nutritious Comfort Food
Unlike classic mac and cheese, this version sneaks in roasted butternut squash, giving you extra fiber, vitamins, and a natural sweetness that balances the richness of the cheese.
Perfect for Portion Control
Since they’re baked into muffin tins, you get ready-made portions. Ideal for meal prep, lunchboxes, or serving at gatherings without the mess of scooping.
Crowd-Pleasing and Kid-Friendly
Even picky eaters love these golden, cheesy cups. They look fun, taste indulgent, and no one realizes there’s a veggie hidden inside.
Make-Ahead Friendly
You can prepare the mac and cheese in advance, spoon it into the cups, and bake right before serving—perfect for busy nights or entertaining.
Customizable Flavors
Add crispy bacon, sautéed spinach, or extra spices to make them your own. The base recipe is flexible and forgiving.

Ingredients

2 cups cooked elbow macaroni (al dente)
1 ½ cups roasted butternut squash puree
2 tbsp unsalted butter
2 tbsp all-purpose flour
2 cups milk (warm)
1 ½ cups sharp cheddar cheese (shredded)
½ cup Parmesan cheese (grated)
½ tsp garlic powder
½ tsp smoked paprika
Salt and black pepper, to taste
1 large egg, lightly beaten
½ cup breadcrumbs (optional topping)

Instructions

Preheat oven to 375°F (190°C). Grease a 12-cup muffin tin.
Cook pasta until al dente. Drain and set aside.
In a saucepan, melt butter, then whisk in flour to form a roux.
Slowly whisk in warm milk until smooth and thickened.
Stir in squash puree, cheddar, Parmesan, garlic powder, paprika, salt, and pepper. Mix until creamy.
Stir in the cooked macaroni. Let cool slightly, then mix in beaten egg for binding.
Spoon mixture into muffin cups, pressing down gently. Sprinkle breadcrumbs if desired.
Bake 20–25 minutes until golden and set. Let cool 5 minutes before removing.

Assembly Notes

Make sure the mixture is slightly cooled before adding the egg, or it may scramble.
Press pasta firmly into muffin tins so the cups hold their shape.
Allow them to rest a few minutes before removing to prevent breaking apart.

Mistakes to Avoid

Overcooking Pasta: It will turn mushy once baked; keep it slightly firm.
Too Watery Squash: Drain excess liquid from puree or sauce will be runny.
Skipping the Egg: The egg is essential for binding the cups. Without it, they may fall apart.
Removing Too Soon: Let them rest after baking, or they’ll crumble.

Expert Tips

Roast your butternut squash instead of boiling—it adds depth and caramelized sweetness.
Use a mix of cheeses (Gruyère, mozzarella, or fontina) for a more complex flavor.
Line muffin tins with parchment or silicone liners for easy removal.
Freeze extra cups in an airtight container; reheat in the oven for best texture.

FAQs

1. Can I make these without eggs?
Yes, but you’ll need a binder like flaxseed meal + water or extra cheese to help them hold shape.

2. Can I use canned butternut squash puree?
Absolutely, just make sure it’s not too watery. If it is, cook it down on the stove first.

3. How long do these last in the fridge?
They keep well for 3–4 days in an airtight container. Reheat in the oven to crisp them back up.

4. Can I freeze them?
Yes! Freeze baked cups for up to 2 months. Thaw in the fridge, then warm in the oven.

5. What pasta works best?
Elbow macaroni is classic, but small shells or cavatappi also work great.

6. How do I make them gluten-free?
Use gluten-free pasta and substitute rice flour or cornstarch for the roux.