Did you know you can make a rustic pasta dish even better than Trader Joe's butternut squash mac and cheese at home? This copycat butternut squash mac and cheese is easy to make and goes great with some jalapeno cheddar sourdough!

With so many mac and cheese recipes out there, it can be hard to find one that really shines, but this copycat Trader Joe's butternut squash mac and cheese doesn't disappoint!
Ingredients like butternut squash, sage, nutmeg, and roasted garlic make this pasta dish so earthy and flavorful, perfect for those blustery days! If you love unique mac and cheese recipes, bookmark this smoked mac and cheese for next time!
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😍 Why You'll Love This Recipe
- This mac and cheese is the perfect side to serve on holidays like Thanksgiving, Christmas, Halloween, etc.
- The addition of butternut squash elevates this from a simple mac and cheese to a standout side dish!
- You only need simple, inexpensive ingredients for this cost-efficient dish. You probably have most of the ingredients already!
- The blended squash acts as a béchamel, thickening the sauce without any flour! In other words, the only gluten in this recipe is the pasta, which can easily be swapped for a gluten-free alternative.
🔖 Ingredients & Substitutions
- Pasta: Trader Joe's butternut squash mac and cheese is made using rigatoni, so that's what I've used as well. You can also use cavatappi, macaroni, penne, fiocchetti, gigli, fusilli, or your preferred pasta shape.
- Butternut squash: You can use cubed butternut squash, but I personally think it's better when using a whole squash. You can also use acorn squash or pumpkin.
- Milk: Or half & half.
- Garlic: You can use garlic powder if you absolutely must, but roasting a whole head of garlic gives this pasta a unique, complex flavor that really makes the dish, in my opinion.
- Yellow onion: You can also use shallots, red onion, or white onion.
- Mustard: I like to add stone ground mustard to give it a little zing, but you can use Dijon mustard, yellow mustard, honey mustard, mustard powder, etc.
- Cheese: Trader Joe's and I both use a combination of cheddar cheese, gouda, and parmesan cheese, but you could also use gruyere, mozzarella, white cheddar, American, fontina, etc.
- Herbs: Sage, thyme, rosemary, and parsley are all good additions, but I just stick to sage & thyme.
- Seasonings: salt, cayenne, smoked paprika, nutmeg,
- Garnish ideas (optional): Truffle oil, pepitas, red pepper flakes, fried sage leaves, chopped parsley, chives, chili crisp, balsamic glaze, breadcrumbs.
*See recipe card for full list of ingredients
🧀 How to Make Trader Joe's Butternut Squash Mac and Cheese
Preheat oven to 450°F
Step 1: Chop ends off butternut squash, then slice into quarters and scoop out the seeds. Add to a parchment paper-lined baking sheet, along with halved onion and rub them with olive oil. Chop the top off a head of garlic, then add to tray and drizzle with remaining olive oil. Roast in the oven for 30-40 minutes or until fork-tender.
Step 2: Boil pasta according to package instructions. When noodles are al dente, drain, reserving 2 cups of pasta water for the sauce.
Step 3: Allow 4 tablespoon of butter to brown slightly over medium-low heat, stirring often. Reduce heat to low and add 7 sage leaves, frying for about 30-60 seconds. Remove sage and drizzle infused butter over pasta, then gently stir to coat noodles.
Pro Tip: The sage leaves should be nice and crispy. I recommend setting them aside and using them as a garnish later!
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Step 4: Chop squash into cubes, then add to a large bowl (or blender) along with roasted garlic cloves (peeled), onion, fresh thyme, 3 fresh sage leaves, smoked paprika, cayenne pepper, nutmeg, mustard, milk, and pasta water. Blend until smooth.
Step 5: Reduce heat to low and add sauce to pasta, gently stirring until incorporated. Shred cheddar, gouda, and parmesan and mix in until combined.
Step 6: Serve in individual bowls and top with more shredded cheese, pepitas, red pepper flakes, and a small swirl of truffle oil (optional).
🍽️ Serving Suggestions
This Trader Joe's butternut squash mac and cheese goes great with air fried Cornish hens, baked turkey legs, smoked chicken thighs, or smoked pork loin.
Serve alongside other sides like goat cheese salad, roasted rainbow carrots, roasted pumpkin soup, roasted beetroot salad, or dill potato salad.
If you enjoy this recipe, try this air fryer spaghetti squash!
🤷🏻♀️ Recipe FAQs
You don't need to peel butternut squash before roasting it, but you might want to, depending on your preferences. The skin will soften as it roasts, but if the texture bothers you, you can remove it before transferring to the oven.
You can doctor up your butternut squash mac & cheese with some truffle oil, chili crisp, hot sauce, chives, parsley, crispy fried sage, red pepper flakes, pumpkin seeds, or balsamic glaze.
👩🏻🍳 Pro Tips
- Want to make it high protein or gluten-free? Use chickpea pasta instead of rigatoni!
- After roasting, let your veggies cool slightly before cutting & blending so the steam can escape.
- Instead of tossing the seeds, you can use them to make spicy roasted pumpkin seeds.
- I recommend shredding blocks of cheese rather than buying the cheese pre-shredded, as this usually results in a creamier, less stringy texture.
- Finish it off with a high-quality truffle oil. Cheap truffle oils tend to have an artificial taste that can ruin an entire dish!
🍝 More Delicious Pasta Recipes
📖 Recipe
Copycat Trader Joe's Butternut Squash Mac and Cheese
Ingredients
- 1 medium butternut squash (about 4 cups when cubed)
- 1 large yellow onion
- 1 tablespoon olive oil
- 1 garlic head
- 1 lb rigatoni pasta
- 4 tablespoon unsalted butter
- 10 fresh sage leaves (divided)
- 2 cups pasta water
- ½ teaspoon fresh thyme
- 1 teaspoon smoked paprika
- ¼ teaspoon cayenne pepper
- ¼ teaspoon nutmeg
- 2½ teaspoon sea salt
- 2 teaspoon stone ground mustard
- 1 cup milk
- 3 cups cheddar cheese (shredded)
- 3 cups gouda cheese (shredded)
- 3 cups parmesan cheese (shredded)
Garnish Ingredients
- pepitas
- red pepper flakes
- truffle oil
Instructions
- Chop ends off butternut squash, then slice into quarters and scoop out the seeds. Add to a parchment paper-lined baking sheet, along with halved onion and rub them with olive oil. Chop the top off a head of garlic, then add to tray and drizzle with remaining olive oil. Roast in the oven for 30-40 minutes or until fork-tender.
- Boil pasta according to package instructions. When noodles are al dente, drain, reserving 2 cups of pasta water for the sauce.
- Allow 4 tablespoon of butter to brown slightly over medium-low heat, stirring often. Reduce heat to low and add 7 sage leaves, frying for about 30-60 seconds. Remove sage and drizzle infused butter over pasta, then gently stir to coat noodles.
- Chop squash into cubes, then add to a large bowl (or blender) along with roasted garlic cloves (peeled), onion, pasta water, fresh thyme, 3 fresh sage leaves, smoked paprika, cayenne pepper, nutmeg, salt, mustard, and milk. Blend until smooth.
- Reduce heat to low and add sauce to pasta, gently stirring until incorporated. Shred cheddar, gouda, and parmesan and mix in until combined.
- Serve in individual bowls and top with more shredded cheese, pepitas, red pepper flakes, and a small swirl of truffle oil (optional).
Notes
- The sage leaves should be nice and crispy after frying in butter. I recommend setting them aside and using them as a garnish later!
- Want to make it high protein or gluten-free? Use chickpea pasta instead of rigatoni!
- After roasting, let your veggies cool slightly before cutting & blending so the steam can escape.
- Instead of tossing the seeds you can use them to make these spicy roasted pumpkin seeds.
- I recommend shredding blocks of cheese rather than buying the cheese pre-shredded, as this usually results in a creamier, less stringy texture.
- Finish it off with a high-quality truffle oil. Cheap truffle oils tend to have an artificial taste that can ruin an entire dish!
Nena Sterner says
Thank you for sharing this great recipe, we loved it!