Baked pastas are the epitome of autumn or winter comfort food and this Baked Butternut Squash Mac and Cheese is an incredibly easy recipe you'll want to keep in your back pocket. No roux is needed and a list of simple ingredients pave the way for a main dish that is baked with cheesy goodness while celebrating seasonal squash. Scroll down to see how we make it and don't miss the tips and substitutions so can easily customize this to be your new family favorite recipe.

What Makes This Mac n Cheese Recipe the Ultimate Comfort Food
This Butternut Squash Mac and Cheese is packed with flavor and yet doesn't contain a lot of heavy cream or butter. I love making this with the butternut squash I'll pick up at the Napa Farmers Market. We're crafting a creamy cheese sauce without all the extra cheese though we're using a flavor Point Reyes Cheese Toma for this recipe. In lieu of a béchamel sauce, we're relying on the creaminess of puréed butternut squash to make this easy mac and cheese. You'll appreciate the versatility of this dish and the ways you can customize your homemade mac and cheese for the ultimate comfort food without all the extra steps.
Ingredients We'll Need for this Baked Mac and Cheese Recipe with No Roux
To create the appearance of a creamy sauce, we're simmering butternut squash cubes in vegetable or poultry stock. To give added flavor to our squash, we'll rely on aromatics like garlic, shallots, fresh herbs, and some crushed red pepper flakes for a touch of warmth. Dried pasta, créme fraîche, and grated cheese helps us craft a light, cheesy sauce for our delicious mac and cheese. Breadcrumbs add texture to round out this delightful dish. Scroll down for the full recipe card to make this tonight!



How to Make this Baked Butternut Squash Mac and Cheese
This creamy mac and cheese is ready in just under an hour. Here's how we make it:
- Start by preheating oven to 400 degrees Fahrenheit. Generously grease a 9 x 12 baking dish with butter and set to the side.
- In a large 4-quart Dutch oven or heavy bottom pot, heat 2 tablespoons olive oil over medium heat. Add the shallots and cook until translucent, about 3 to 5 minutes. Add the garlic and stir for one minute until fragrant. Add the butternut squash cubes followed by the stock and bring to a quick boil over high heat followed by simmering on medium-low heat. Add the herbs and red pepper flakes, if using, and simmer until squash is tender, about 7 to 10 minutes.
- While the squash simmers, bring a separate pot of salted water to boil. Add in the dried pasta like macaroni noodles or elbow macaroni and cook until just al dente, about 6 minutes.
- Once the squash is tender, remove from heat and, using an immersion blender (or a standalone blender), blend mixture until smooth. Add in the créme fraîche, nutmeg, and half of the grated cheese. Stir to allow the cheese to begin to melt into the sauce.
- Pour sauce over the pasta and stir to combine. Pour into the prepared baking dish. Sprinkle remaining cheese and breadcrumbs over the top.
- Bake for 30-40 minutes until edges are golden and cheese is bubbly and melty. Garnish with fresh herbs and serve.

Key Tips and Substitutions
This is one of the best baked mac and cheese recipes I've made to date. What I love about it is how versatile it can be. Here are a couple of key tips and substitutions or swaps you can make:
- When it comes to the best cheese to use, use what you like and one that is a melty cheese variety. Types of cheese options to try include gouda, Gruyère, or a sharp cheddar cheese with a mix of pre-shredded cheese like mozzarella. I personally love the Toma and will use a mix of Toma with the Toma Herbs de Provence.
- For the squash: you can use puréed honeynut, Autumn Frost, Kabocha, or Black Futsu winter squash. You want a squash whose flesh you can cook down to purée. For some squash, you can take an extra step to roast the flesh in the squash without peeling. Then, scoop the flesh and combine with the aromatics and stock as described above. You can also opt for pre-cut squash cubes from your local grocery store to save a step in meal prep.
- For the pasta: you can also use fresh pasta! If opting to do this, no need to cook them ahead of time. You can simply toss the sauce together with the fresh pasta and then bake just as described above.
- On the breadcrumbs: you can use store bought or homemade for the crunchy topping. I have used rosemary sourdough and brioche bread crumbs for this crispy top topping. All are good options.
- Store leftover mac and cheese in an airtight container in the refrigerator for up to 5 days. To reheat for best results, reheat in a 350 degree oven until warmed through.
More Pasta Dishes to Enjoy

Baked Butternut Squash Mac and Cheese
Equipment
- 1 shallow baking dish, measuring 10.5' by 7.5'
Ingredients
- 4 cups once cubed butternut squash from one medium sized squash ¼ cup chopped shallots 4 cloves garlic peeled
- 2 tablespoons olive oil
- 2 teaspoons chopped fresh herbs such as thyme sage, parsley
- ⅛ teaspoon crushed red pepper flakes optional
- 2 to 3 cups vegetable or poultry stock you want enough to make a smooth consistency for the sauce
- 1 teaspoon kosher salt
- ⅛ teaspoon ground nutmeg
- ¼ teaspoon ground black pepper
- ¼ cup
créme fraîche
- 2 cups grated Toma cheese can also use gruyere or fontina
- ¾ cup toasted breadcrumbs
- 2 tablespoons butter
- 1 pound
dried pasta shape of choice
you can also use 12 ounces fresh pasta - Garnish options: grated parmesan chopped fresh herbs like chives, parsley, thyme
Instructions
- Preheat oven to 400 degrees Fahrenheit. Generously grease a 9 x 12 baking dish with butter and set to the side.
- In a large 4-quart Dutch oven or heavy bottom pot, heat 2 tablespoons olive oil over medium heat. Add the shallots and cook until translucent, about 3 to 5 minutes. Add the garlic and stir for one minute until fragrant. Add the butternut squash cubes followed by the stock and bring to a quick boil followed by simmering. Add the herbs and red pepper flakes, if using, and simmer until squash is tender, about 7 to 10 minutes.
- While the squash simmers, bring a separate pot of salted water to boil. Add in the dried pasta like macaroni noodles or elbow macaroni and cook until just al dente, about 6 minutes.
- Once the squash is tender, remove from heat and, using an immersion blender (or a standalone blender), blend mixture until smooth. If the mixture feels a bit too thick, add in ¼ cup of stock at a time until consistency is smooth.
- Add in the créme fraîche, nutmeg, and grated cheese. Stir to allow the cheese to begin to melt into the sauce.
- Pour sauce over the pasta and stir to combine. Pour into the prepared baking dish. Sprinkle remaining cheese and breadcrumbs over the top.
- Bake for 30-40 minutes until edges are golden and cheese is bubbly and melty. Garnish with fresh herbs and serve.









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