Preheat oven to 425°F. Slice butternut squash in half lengthwise. Coat each cut side with cooking spray. Place squash halves, cut side down, on foil-lined baking sheet. Bake at 425°F for 45 minutes. Let stand at room temperature 20 minutes. Scoop out 2 1/2 cups flesh. Set aside.
Heat oil in a Dutch oven over medium. Add onion and carrots; cook 5 minutes or until tender. Add garlic, nutritional yeast, dry mustard, salt, pepper, and Dijon mustard; cook, stirring often, 2 minutes or until aromatic. Add beer; bring to a boil, scraping pan to loosen browned bits. Cook 5 minutes or until liquid is reduced by half. Reduce heat to medium, and stir in squash, stock, and milk.
Pour mixture into a blender. Remove center piece of blender lid (to allow steam to escape); secure lid on blender. Place a clean towel over opening in lid. Process until smooth. Pour mixture back into Dutch oven.
Combine cornstarch and 2 tablespoons water in a small bowl; mix well. Whisk cornstarch mixture into soup; cook 5 minutes, stirring often, until soup begins to thicken. Add cheese, stirring until cheese melts and mixture is smooth. Ladle soup evenly into each of 6 bowls. Top each serving with 1 teaspoon pumpkin seeds.
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