Preheat your oven to 425°F. Line a baking sheet with parchment paper and grease a 9x13-inch baking dish.
Halve the butternut squash lengthwise, scoop out the seeds, drizzle with olive oil, and sprinkle with sea salt and black pepper. Place cut side down on the baking sheet.
Wrap the chopped shallots in foil and place on the baking sheet with the squash. Roast everything for 30 to 45 minutes until the squash is tender.
In a small bowl, mix panko breadcrumbs with a drizzle of olive oil for the topping.
Cook pasta in salted boiling water according to package instructions, reserving 1 1/2 cups of pasta water before draining.
Scoop about 2 cups of the cooked squash flesh into a blender. Add reserved pasta water, roasted shallots, olive oil, balsamic vinegar, sea salt, onion powder, garlic powder, sage, nutmeg, and black pepper. Blend until smooth.
In the same pot used for pasta, heat the almond milk over medium heat. Stir in the blended squash sauce and cook for about 3 minutes.
Gradually whisk in the cheddar, Gruyere, and pecorino cheeses until melted and creamy.
Fold the cooked pasta into the cheese sauce until evenly coated.
Transfer the mixture to the prepared baking dish and sprinkle the panko topping on top.
Broil under the oven’s broiler for 5 to 10 minutes until the topping is crispy and golden brown.
Let it sit for 15 minutes before serving to allow it to set.
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Notes
Store leftovers in an airtight container in the refrigerator for up to three days.