Preheat oven to 350ºF degrees. Line a 12-count muffin pan with cupcake liners.
In a mixing bowl, whisk together the flour, baking powder, baking soda, spices, and salt until combined; set aside.
In the bowl of a stand mixer fitted with a paddle attachment, beat the butter and sugar together on medium speed until lightened and creamy. Beat in the eggs, one at a time, until combined, scraping down the sides and bottom of the bowl as needed. Beat in the Greek yogurt and vanilla on medium speed.
Pour the dry ingredients into the wet ingredients and mix until combined. Add the eggnog, then mix until just combined, scraping down the sides and bottom of the bowl as needed.
Fill cupcake liners 2/3 of the way full. Bake for 19-22 minutes or until a toothpick inserted in the center comes out clean or with few crumbs attached. Allow to cool in the pan for 5 minutes before transferring to a wire rack to cool completely.