Melt the butter over low heat. Stir in the leeks and cook until softened, 4 to 6 minutes.
Add the zest, squash, and nutmeg and cook for 2 minutes.
Add the stock and bring to a boil. Simmer over medium heat, covered, until squash is tender, about 15 to 20 minutes.
Puree in a food processor or blender in two batches. Season with ½ teaspoon salt and ¼ teaspoon pepper.