Trader Joe’s Butternut Squash Mac and Cheese

There’s something about the cozy, cheesy comfort of mac and cheese that just hits differently once fall rolls around. This homemade version of Trader Joe’s Butternut Squash Mac and Cheese has become a go-to in my kitchen — creamy, savory, a little earthy, and perfect for warming up chilly evenings. Even better, it’s a sneaky way to get more veggies in without anyone at the table noticing.

Why I Started Making This Butternut Squash Mac at Home

Mac and cheese at Thanksgiving? That’s a solid yes from me. We added it to our holiday table a few years back, and now I can’t imagine the meal without it. There’s something magical about a scoop of cheesy pasta sitting next to roasted turkey and cranberry sauce.

I’ll admit, I was late to the butternut squash mac party. I used to roll my eyes at it, thinking, “Really? Veggies in mac and cheese?” But everything changed the day I tried the frozen version from Trader Joe’s — just out of curiosity during a grocery run. I heated it up, took one bite, and instantly got it. It wasn’t “veggie mac and cheese.” It was just really good mac and cheese, with an extra depth of flavor I wasn’t expecting.

So, I set out to make a version at home — one that felt a little more special and didn’t come out of a microwave. This version hits all the right notes: velvety sauce, hearty pasta, loads of cheese, and a golden crunchy topping. It’s a cozy dinner win that even the pickiest eaters in my house love.

What You’ll Need

Here’s a breakdown of what goes into this comfort-packed casserole. I’ve played around with a few combinations, so feel free to tweak it to what you’ve got on hand.

Pasta and Veggies

• Pasta: I used chickpea pasta this time because I had it in the pantry and like the extra protein, but regular elbow or shell pasta will do the trick.
• Onion: White onion gives a subtle sweetness, but red onion works too if you like a stronger flavor.
• Mushrooms: I sneak these in because once they’re sautéed and coated in sauce, they vanish into the mix — flavor without fuss.

Creamy Butternut Cheese Sauce

• Butternut Squash: A medium one, peeled, cubed, and roasted until tender. Roasting gives it that natural sweetness and a richer flavor.
• Fresh Thyme: I always reach for fresh herbs when I can — the aroma alone is worth it.
• Vegetable Broth: Helps loosen up the sauce to a pourable consistency.
• Cheese: I like using a mix — aged gouda adds depth, mozzarella gives you that nice stretch, and provolone melts like a dream. Use whatever combo you love.
• Nutritional Yeast (optional): A spoonful adds a savory, nutty note that really works here.

Topping (The Crunchy Part)

• Crackers: Crushed Trader Joe’s cornbread crisps are fantastic, but you could use breadcrumbs, Ritz, or even Cheez-Its.
• Extra Cheese: Because more cheese on top is always a good idea.

Let’s Cook: Step-by-Step

1. Roast the Squash

Preheat the oven to 375°F. Peel the squash, remove the seeds, and dice into small cubes. Toss with a little oil, salt, and pepper. Roast for about 35 minutes until soft and slightly caramelized. Don’t turn the oven off — you’ll use it again soon.

2. Boil the Pasta

Cook your pasta according to the package instructions, but save about a cup of that starchy pasta water before draining — it’ll help your sauce cling beautifully to the noodles.

3. Sauté the Veggies

While the squash roasts and pasta boils, sauté the onion in a little butter. Once softened, add in the mushrooms (or any other veggie you like — spinach, bell peppers, broccoli, go wild). Cook until tender and set aside.

4. Blend the Sauce

In a saucepan, melt a bit of butter and add your roasted squash, thyme, a splash of hot sauce (if you like a tiny kick), and that saved pasta water. Use an immersion blender (or regular blender) to purée until smooth, adding broth as needed to thin it.

Stir in your cheese and nutritional yeast. If it gets too thick, add a bit more broth. The sauce should be silky and pourable — not runny, but not gloopy either.

5. Bring It All Together

Grease a 9×13″ baking dish. Toss in your cooked pasta, the sautéed veggies, and pour the butternut cheese sauce over everything. Mix well so it’s all coated and cozy.

6. Top and Bake

Sprinkle on the remaining cheese and your crushed crackers. Bake for 15–18 minutes, then broil for 2–3 minutes to get that irresistible golden top.

This dish smells incredible coming out of the oven — like comfort in a casserole.

Helpful Tips From My Kitchen

• Roast extra squash: If you’ve got a big one, roast the extra and save it for soups, risotto, or even a mash for baby food.
• Use what’s in your fridge: I’ve made this with leftover kale, zucchini, or bell peppers. It’s pretty forgiving.
• Make it gluten-free: Swap in gluten-free pasta and crackers, and you’re good to go.
• Cheese tip: Grate it fresh if you can — pre-shredded bags often have additives that prevent melting smoothly.

Make It Ahead

You can absolutely prep this earlier in the day. Just assemble everything up to the baking step, cover, and refrigerate. When you’re ready to eat, bake as directed (maybe add a few extra minutes if it’s straight from the fridge).

Leftovers? They reheat well in the microwave or oven. Add a splash of milk if it feels a little dry.

How I Like to Serve It

This is one of those dishes that can stand on its own — just serve it up in a bowl and call it a night. But I also love pairing it with a simple arugula salad with lemon vinaigrette to balance the richness.

It’s great as a vegetarian main or a hearty side for roasted chicken or turkey. I’ve even packed the leftovers into lunchboxes for the next day, and they come back empty.

Storage Notes

Store leftovers in an airtight container in the fridge for up to 4 days. To reheat, warm it gently in the microwave or oven with a splash of broth or milk.

You can freeze it too — just skip the cracker topping, or add it fresh when reheating.

Yield: 8

Trader Joe's Butternut Squash Mac and Cheese

Print

Cozy, creamy, and full of flavor—this butternut squash mac and cheese is the ultimate comfort dish. It’s a sneaky way to add veggies into a cheesy pasta bake that both kids and adults will love. Perfect for fall, weeknights, or even your Thanksgiving table.

Prep Time 10 minutes

Cook Time 50 minutes

Total Time 1 hour

Ingredients

• 1 medium butternut squash, peeled and cubed
• Olive oil or cooking spray
• 8 oz pasta (chickpea pasta like Banza works great)
• ½ cup reserved pasta water
• ½ cup diced white onion
• ¼ cup finely chopped mushrooms
• 1 tablespoon butter
• 4 sprigs of fresh thyme
• 1 cup vegetable broth (plus more as needed)
• 1 teaspoon hot sauce
• 2 tablespoons nutritional yeast
• 1¾ cups shredded cheese (cheddar, gruyère, or a mix)
• 1 cup crushed crackers (for topping)
• Salt and pepper, to taste

Instructions

1. Start by roasting the squash. Preheat your oven to 375°F and line a baking sheet with foil or parchment paper. Spray lightly with oil.
2. Peel and deseed the butternut squash, then chop it into small cubes. Spread them out on the prepared sheet, toss with oil, salt, and pepper, and roast for about 35 minutes, or until fork-tender. Keep the oven on—your mac and cheese is going in next.
3. Meanwhile, bring a pot of salted water to a boil and cook the pasta until al dente. Reserve about half a cup of the starchy pasta water before draining.
4. While that’s happening, melt butter in a skillet over medium heat. Add the onion and sauté for a few minutes until soft and translucent. Stir in the mushrooms and cook until tender. Feel free to toss in any extra veggies you love—spinach, bell pepper, or broccoli all work well. Once softened, remove from heat and set aside.
5. To make the cheese sauce, warm a sauce pot over medium heat and melt a bit more butter. Add the roasted squash, thyme leaves (stripped from stems), hot sauce, and the reserved pasta water. Blend with an immersion blender until it starts coming together. Slowly pour in the broth, a little at a time, blending between additions, until smooth and creamy.
6. Stir in the nutritional yeast and shredded cheese. If it looks a bit chunky, pulse it all in a blender or food processor for a silky finish.
7. Now for the fun part—assembling! Lightly grease a 9x13-inch baking dish and pour in the cooked pasta. Add the sautéed veggie mixture, then pour the creamy squash cheese sauce over everything. Stir well so it’s evenly coated.
8. Top with a handful of shredded cheese and sprinkle the crushed crackers on top.
9. Bake uncovered for 15–18 minutes until bubbly and heated through. For that irresistible golden top, broil for 2–3 minutes right at the end.

Notes

• Keep leftovers in an airtight container in the fridge for up to 5 days. Reheat in the microwave with a splash of milk or a small pat of butter to keep it creamy.

Nutrition Information

Yield

8

Serving Size

1
Amount Per Serving Calories 245Total Fat 14gSaturated Fat 6gTrans Fat 0gUnsaturated Fat 6gCholesterol 28mgSodium 345mgCarbohydrates 21gFiber 3gSugar 2gProtein 10g

dinnerbytes.com, occasionally offers nutritional information for recipes contained on this site. This information is provided as a courtesy and is an estimate only. This information comes from online calculators. Although dinnerbytes.com attempts to provide accurate nutritional information, these figures are only estimates.

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Questions I Get a Lot

Can I make this without a blender?
You could mash the squash with a fork or potato masher, but the sauce will be chunkier. A blender really gives you that silky texture.

Is there a cheese substitute if I don’t have gouda?
Totally. Try sharp cheddar, fontina, or even a bit of parmesan if that’s what you have on hand.

Does it taste like squash?
Not really. The squash gives it a creamy, slightly sweet base, but the cheese takes center stage. Most people won’t even realize there are veggies in it.

Try Other Butternut Squash Recipes:

Butternut Squash Quinoa Salad

Roasted Butternut Squash Seeds

Ground Turkey and Butternut Squash