This homemade take on Trader Joe’s Butternut Squash Mac and Cheese is an ideal cozy fall dish. It’s creamy, savory, and cheesy—perfect for a comforting weeknight dinner or to add to a holiday spread. The roasted squash purees into a velvety sauce that mixes seamlessly with pasta and cheese, making it a great way to add extra vegetables to a meal without overwhelming picky eaters.
About this Mac and Cheese
If your family enjoys mac and cheese at holiday meals, this version is a delicious twist. Roasted butternut squash adds natural sweetness and body to the sauce while cheeses give the dish its classic, comforting richness. The finished bake is topped with crunchy crackers or breadcrumbs for texture, and the savory flavors pair well with turkey, stuffing, or roasted vegetables.
I originally didn’t expect much from butternut squash mac and cheese, but after trying Trader Joe’s frozen version I was inspired to recreate it at home. This copycat combines roasted squash, a touch of thyme and hot sauce for depth, and a blend of cheeses that melt into a smooth, satisfying sauce. Kids and adults alike often don’t notice the veggies once everything is layered together—making this a friendly option for families.
Recipe Ingredients
Pasta and Veggie Mixture:
- Pasta: Use your favorite shape—shells or elbows are classic. I used chickpea-based noodles, but regular pasta works great.
- Onion: White onion adds gentle sweetness when sautéed; red onion will give a stronger flavor if preferred.
- Mushrooms: Finely diced and sautéed, they blend into the sauce and add savory depth without being pronounced.
Sauce:
- Butternut Squash: Roasted and pureed until smooth to create the base of the sauce.
- Thyme: Fresh thyme adds a subtle earthy note.
- Vegetable Broth: Used to thin the puree to a creamy sauce consistency.
- Cheese: A blend of shredded cheeses—aged gouda, sharp cheddar, mozzarella or provolone—melts into the squash for a rich finish. Reserve a little for the topping.
Topping:
- Crackers: Crumbled cornbread crisps or any buttery cracker add crunch. Breadcrumbs or crushed crackers also work.
- Cheese: Extra shredded cheese on top helps create a golden, bubbly crust when baked.
See the recipe card below for a full list of ingredients and measurements.
How to Make This Recipe
Step 1: Preheat oven to 375°F. Line a baking sheet with foil and coat with cooking spray or oil. Halve the butternut squash, scoop out seeds, peel, dice into small cubes, toss with oil, salt, and pepper, and roast for about 35 minutes. Keep the oven on for baking the assembled mac later.
Step 2: Cook the pasta according to package directions and reserve about 1/2 cup of the starchy pasta water before draining.
Step 3: While the squash roasts, sauté diced onion in butter over medium heat for 3–4 minutes, then add mushrooms or other vegetables (spinach, red pepper, or broccoli work well). Cook until tender and set aside.
Step 4: For the sauce, melt butter in a saucepan. Add the roasted squash, fresh thyme leaves, hot sauce, and reserved pasta water. Blend with an immersion blender or in a countertop blender until smooth. The puree will be thick—thin it with vegetable broth, adding about 1/4 cup at a time until you reach a creamy consistency.
Stir in nutritional yeast and about 1 1/2 cups shredded cheese until melted and incorporated. If needed, blend again for an extra-smooth texture.
Step 5: Assemble the casserole in a sprayed 9×13″ baking dish. Add the cooked pasta, then the sautéed vegetables, and pour the butternut squash cheese sauce evenly over everything. Stir gently so the sauce coats the pasta and vegetables.
Step 6: Sprinkle the remaining shredded cheese and crumbled crackers or breadcrumbs on top. Bake at 375°F for 15–18 minutes, or until heated through and cheese is melted. Finish under the broiler for 2–3 minutes to achieve a bubbly, golden top. Let rest a few minutes before serving.
Recipe FAQs
Store leftovers in an airtight container in the refrigerator for 3–5 days. Reheat in the microwave for 60–90 seconds, stirring and adding a small pat of butter or a splash of oil if the pasta seems dry.
Yes—thawed frozen squash will work, but roasting fresh squash develops caramelized flavor that enhances the sauce.
Absolutely. Use gluten-free pasta and gluten-free crackers or breadcrumbs for the topping.
Roasted or sautéed vegetables like Brussels sprouts or green beans, a crisp salad, or cooked protein such as grilled chicken, salmon, or tofu make good accompaniments.
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If you enjoyed this recipe, please rate it in the recipe card below. Your feedback is appreciated!
Trader Joe’s Butternut Squash Mac and Cheese Copycat Recipe
Equipment
- Baking sheet
- Cutting board
- Knife
- Vegetable peeler
- Sauce pot
- Skillet
- Strainer
- Cheese grater
- Immersion blender
- Blender or food processor
- 9×13 baking dish
- Mixing spoon
- Measuring cups and spoons
Ingredients
- 1 medium butternut squash
- cooking spray or olive oil
- 8 oz pasta
- ½ cup pasta water
- 1 tbsp butter
- ½ cup white onion, diced
- ¼ cup mushrooms, diced
- 4 stalks fresh thyme
- 1 cup vegetable broth
- 1 tsp hot sauce
- 2 tbsp nutritional yeast
- 1¾ cup shredded cheese
- 1 cup crackers, crushed
Instructions
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Preheat oven to 375°F. Line a baking sheet and prepare the butternut squash by halving, seeding, peeling, and dicing into cubes. Toss with oil, salt, and pepper and roast about 35 minutes.
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Cook pasta according to package directions and reserve ½ cup pasta water before draining.
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Sauté diced onion in butter for 3–4 minutes, add mushrooms or other vegetables, cook until tender, and set aside.
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Make the sauce by combining roasted squash, thyme, hot sauce, and reserved pasta water in a saucepan. Blend until smooth, then thin with vegetable broth in ¼ cup increments until creamy.
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Stir in nutritional yeast and shredded cheese until melted. Blend again if necessary for a smooth sauce.
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Assemble in a 9×13″ dish: pasta, sautéed vegetables, and pour the squash-cheese sauce over top. Mix gently to combine.
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Top with remaining cheese and crushed crackers or breadcrumbs. Bake 15–18 minutes until heated through and cheese is melted. Broil 2–3 minutes for a bubbly top.
Nutrition
Notes
Looking for this in MyFitnessPal?
Search “A Paige Of Positivity” and find Butternut Squash Mac & Cheese nutrition entries. For the most accurate macronutrients, consider entering each ingredient directly into your diary.
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