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Preheat the oven to 400F.
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Add the butternut squash and onion to a large baking dish. Drizzle with oil and season with salt and black pepper.
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Slice the top of the garlic bulb to expose the tops. Place on a piece of foil (that’s large enough to cover the garlic) and drizzle with oil. Wrap the foil over the garlic bulb and then place on the baking sheet. Bake the squash, onion and garlic for 40-45 minutes or until squash is soft and fully cooked.
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In the meantime, in a large pot cook and drain the pasta according to package instructions, reserving ¼ cup of pasta water.
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Once the squash, onion and garlic are soft and roasted, remove from the oven and let them cool for 10 minutes. Once cool enough to handle, add the squash and onion to a high speed blender. Carefully unwrap the garlic from the foil and squeeze the garlic bulb so the garlic pops up. Add to the blender along with the soaked cashews, lemon juice, nutritional yeast, mustard, smoked paprika, cayenne (if using), nutmeg, salt, pepper and milk. Blend until smooth and creamy. If too thick, add 1-2 tbsp reserved pasta water or more as needed. Taste and adjust seasoning as needed.
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Add the cooked drained pasta back to the same pot or a large mixing bowl. Pour the cheese sauce over the pasta and mix to combine.
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Transfer and spread the coated pasta evenly into a greased large baking dish (feel free to use the same one as you used for the roasted vegetables to save on clean-up). Top evenly with the shredded cheese.
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Add the butter, panko crumbs and sage and mix to combine. Sprinkle evenly over the mac and cheese and bake in the oven for 10-12 minutes, or until golden brown.
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Remove from the oven, garnish with some freshly cracked black pepper and a pinch of fresh chopped chives. Serve warm and enjoy.