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Baked Butternut Squash Mac and Cheese is incredibly creamy, flavorful, and easy to make! Made with a creamy butternut squash sauce, cheddar, parmesan, and smoked gouda cheese. Fresh thyme and sage add plenty of flavor, and it’s topped with a crispy, buttery bread crumb topping. This side dish will be the star of your Thanksgiving meal!
Table of Contents
Why you’ll love Baked Butternut Squash Mac and Cheese:
- Super Cheesy Butternut Squash Sauce – This mac and cheese is LEGIT. I mean, we’re using three kinds of cheese, plus a creamy sauce made with butternut squash and fresh herbs.
- Easy Side Dish – Thanksgiving prep was never so easy – or so delicious! Even if you’ve never made homemade mac and cheese before, you can absolutely make this gorgeous side in only about an hour.
- Sure to Please – We finish the dish with a buttery, crispy bread crumb topping that everyone loves. Warning – you may be returning home with an empty dish!
Is mac and cheese part of your Thanksgiving traditions already? It hasn’t been in our house in the past, but now that this recipe exists, it will forever have a place on our table!
Ingredient Overview:
As always, the full recipe with measurements & step-by-step instructions can be found in the recipe card at the bottom of this post. Use the table of contents (back at the top, below the first image, to navigate).
- Butter – I always use salted butter for the best flavor, but feel free to use unsalted butter if you prefer.
- Sage and Thyme – Use both fresh and dried herbs to really bring the cozy fall vibe.
- Butternut Squash – You need 1 large squash to yield a total of 4 cups of cubed squash.
- Broth – Chicken broth or vegetable broth both work!
- Milk – Whole milk or 2% is fine.
- Pasta – Use your choice of small-to-medium sized noodles. I’m using shells here but penne or ziti, large elbow macaroni, or rigatoni are all great options.
- Cheeses – I like using a combination of cheddar, parmesan, and smoked gouda. Buy the cheeses in blocks and grate by hand for the smoothest cheese sauce. The pre-shredded can make the sauce grainy.
- Panko – Use panko bread crumbs instead of regular bread crumbs for a crisp topping.
Recipe Substitutions & Variations:
- Gluten-free – Use your favorite, trusted gluten-free pasta and breadcrumbs. I don’t have enough experience with gf cooking to make a recommendation here so be sure to use a brand of pasta you know is good and won’t turn mushy like some do.
- Dairy-free – I have not tried a dairy-free version of this recipe. Try using your preferred plant-based substitutes, and let me know how it turns out!
- Extra Protein – Add some chopped cooked chicken or bacon to the mac and cheese before baking, if desired.
How to Make Butternut Squash Mac and Cheese:
Step 1: Begin the Butternut Squash Base. Saute fresh herbs in butter with garlic and onion. Add the butternut squash and broth and simmer until the squash is tender.
Stir in the milk and use an immersion blender (or transfer the mixture to a blender) and puree until smooth.
Step 2: Cook Pasta. Follow package directions to cook the pasta, cooking a minute or two under the recommended time (we want it on the al dente side since it’s going in the oven). Drain the pasta.
Step 3: Add the Cheese. Add the sauce back to the dutch oven on medium heat. Stir in the hand-grated cheese a bit at a time. Then stir in the pasta, and a little of the pasta water as needed to help the sauce stick.
To thicken up the sauce, take out several tablespoons of sauce and add to a small bowl. Stir in a few tablespoons of cornstarch. Add back into the pot over medium heat, and stir for a few minutes until it thickens.
Step 4: Assemble. For the bread crumb topping, melt (or brown!) salted butter, and stir in panko breadcrumbs, thyme, and sage. Pour the mac and cheese into a baking dish, add a sprinkle of parmesan, and add the panko topping.
Step 4: Bake. Bake the macaroni and cheese until the topping is crisp and the sauce is bubbling. Broil for 1-2 minutes at the end to brown the top.
Serving + Storing:
Serve immediately while warm and gooey! Baked butternut squash macaroni and cheese is perfect on the Thanksgiving (or any holiday!) table paired with other cozy dishes like my Sweet Potato Casserole with Streusel and my Homemade Green Bean Casserole.
Store leftovers in an airtight container, and keep in the fridge for 3-4 days.
Expert Cooking Tips:
- Oven Thermometer – An oven thermometer will tell you if your oven is actually running at the temperature you set it to. Your oven may not be accurate. Accurate oven temperature is crucial for most bakes, so I leave an oven thermometer in at all times to keep an eye on my oven’s calibration.
- Grate the Cheese – It’s important to do this by hand because pre-shredded cheese has anti-caking agents that will cause your cheese sauce to clump or become gritty.
- Make Ahead – You can prep the butternut mac and cheese without the bread crumbs a day ahead, store it in the fridge with the lid on, and then add the topping and bake it the day of Thanksgiving!
FAQs:
Use a vegetable peeler to remove the thick skin. Cut the squash in half, length-wise, and scoop out the seeds. Then chop into cubes that are uniform in size. Some grocery stores also sell it pre-cut!
It has that irresistible coziness of traditional macaroni and cheese, with lots of rich and gooey cheesy goodness. Adding pureed butternut squash makes the casserole slightly sweet, but the cozy herbs balance that sweetness with a savory flavor.
Special Tools:
- Dutch Oven – A deep heavy-bottomed pan is ideal for sautéing and creating a luscious sauce or gravy.
- Immersion Blender – Using an immersion blender is by far the most fast and easy way to puree a large batch of butternut squash sauce. You can also use a blender that is safe for high heat, working in batches.
More Comfort Food Recipes to Love:
- Cheesy Pasta Bake with Sausage and Peppers
- Chicken Wild Rice Casserole
- Creamy Butternut Squash Pasta with Pancetta
- Best Ever Stuffed Acorn Squash
- White Cheddar Mac and Cheese with Brown Butter Breadcrumbs
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Baked Butternut Squash Mac and Cheese
Ingredients
For the Butternut Squash Sauce
- 1/4 cup salted butter, 57 grams
- handful of fresh sage + thyme
- 1/2 yellow onion, diced
- 4 large cloves garlic, minced
- 4 cups butternut squash, peeled and cubed, 1 large squash should yield this much
- 1 and 1/2 tsp dried thyme
- 1 and 1/2 tsp dried sage
- 1-2 tsp salt
- 1/2 tsp pepper
- 1 and 1/2 cups chicken broth, Or vegetable broth!
- 2 cups milk, 480 mL
- 1 pound pasta , 16 ounces/454 grams
- 12 ounces cheddar cheese,, See Note Below
- 1 and 1/2 cups parmesan, divided
- 7 ounces smoked gouda, in block form, See Note Below
- 1/4 cup corn starch, 32 grams
For the Breadcrumb Topping
- 1 cup panko bread crumbs
- 1/4 cup salted butter, melted or browned, See Note. 56 grams.
- pinch of thyme + sage
Instructions
- Make the Butternut Squash Sauce: Add the butter to a large dutch oven over medium heat. While it's melting, toss in the handful of fresh sage and thyme, and stir, sautéing for a minute. Remove the herbs, reserve them for later. Add the onion and garlic, and continue sautéing until softened. Add the butternut squash and the dried sage, thyme, salt, and pepper. Stir to combine everything. Add broth and the reserved herbs we sautéed in butter earlier, and bring to a boil. Once boiling, reduce heat to low and simmer for 8-10 minutes, stirring occasionally, until the squash is tender. Remove the herbs and discard. Stir in the milk and use an immersion blender (or transfer the mixture to a blender) and puree until smooth. Return sauce to the pot and keep it off the heat while you get the pasta cooking.1/4 cup salted butter, handful of fresh sage + thyme, 1/2 yellow onion, diced, 4 large cloves garlic, minced, 4 cups butternut squash, peeled and cubed, 1 and 1/2 tsp dried thyme, 1 and 1/2 tsp dried sage, 1-2 tsp salt, 1/2 tsp pepper, 1 and 1/2 cups chicken broth, 2 cups milk
- Cook Pasta: Bring a large pot of salted water to a boil, then cook pasta according to package directions, but cook it just a minute or two under the recommended time (we want it on the al dente side since it's going in the oven). Continue making the sauce while the pasta cooks – see the step below. Save 1/2 cup of the pasta water, then drain the pasta and set aside.1 pound pasta
- Finish the Sauce: While the pasta cooks, add your pureed sauce back to the dutch oven on medium heat. Grate the cheese – it's important to use blocks of cheese and not pre-grated which can make a gritty sauce. Add the cheese, remembering to reserve 1/2 cup of the parmesan for the top, a handful at a time, stirring well between each addition to ensure it melts smoothly. Stir in the pasta, and a little of the pasta water as needed to help the sauce adhere to the pasta. Taste and add more seasoning as desired. To thicken up the sauce, take out 1/3 cup + 1 tbsp of sauce and add to a small bowl. Add 3 tbsp cornstarch and stir until completely mixed into the sauce. Add back into the pot while still over medium heat, and stir for a few minutes until it thickens up a bit.12 ounces cheddar cheese,, 1 and 1/2 cups parmesan, divided, 7 ounces smoked gouda, in block form, 1/4 cup corn starch
- Assemble & Make Breadcrumb Topping: Preheat oven to 350℉. Spray a 9×13 pan with nonstick spray. Add the mac and cheese. Top with the remaining parmesan. Stir together the melted butter, panko, and a pinch of thyme, salt, and sage and sprinkle over the top of the mac and cheese.1 cup panko bread crumbs, 1/4 cup salted butter, melted or browned, pinch of thyme + sage
- Bake: Bake for 15 minutes – the cheese should be a little bubbly – and broil 1-2 minutes at the end to brown the breadcrumbs.
- Serve + Store: Serve immediately! Store leftovers, tightly covered, in the fridge for up to 6 days.
- Make Ahead Tips: The sauce base (without the cheese added) can be made 1-2 days ahead and kept in the fridge until ready to finish making. The whole dish, without the bread crumb topping, can be made and stored in the baking dish, covered well, in the fridge for 1-2 days before topping with the breadcrumbs and baking.
Notes
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
Made this for Thanksgiving and it was quickly devoured by all, including my picky kids and husband who isn’t a butternut squash fan! We smoked the Mac and cheese and it totally took it to another level in flavors! Lots of work making the sauce, but well worth it.
Wow, it looks like half your Thanksgiving menu was my recipes – I’m so flattered!! 🙂 Thanks for taking the time to leave comments on all the recipes you tried – I greatly appreciate that! And I’m happy to hear you enjoyed this mac and cheese, too!
Really tasty!! Made it using a third of the ingredients and it fed three of us as a main meal. Will definitely be making it again in the future!
So glad you liked this, Annie! 🙂
Oh wow… never tried pumpkin mac&cheese. But now I definitely must make it and give it a try. This recipe sounds so delicious and looks so tasty. My family will love this too I’m sure!
Mac and cheese is such a crowd pleaser and I can’t believe I’ve never thought to make it with a butternut squash sauce. This looks amazing and would make the perfect side dish for the holidays!
This dish sounds like the perfect fall comfort food. I’ve just printed the recipe so that I can make it this weekend. This is the weekend we put up our Christmas tree, and think this dish will add the right finish to a day of decorating.