Preheat the oven to 350 degrees F. Line a cupcake tin with liners.
In a bowl, whisk together the flour, baking soda, cinnamon, salt and nutmeg. Note: If you LOVE spice, feel free to add some extra spice in here (pumpkin! allspice! more cinnamon! - you can add another 1/2 to 1 teaspoon if you'd like) as this isn't overly spiced. I prefer less spice in my pumpkin.
In a large bowl, whisk together the pumpkin, sugar, yogurt and oil. Once smooth and combined, whisk in each egg one at a time. Whisk in the vanilla extract.
Add the dry ingredients to the wet, mixing until combined and no large lumps remain.
Fill the cupcake liners ¾ of the way full. Bake for 28 to 32 minutes, or until a tester inserted in the center of the cupcakes comes out clean.
Cool the cupcakes completely. Frost with the coffee cream cheese frosting. Serve!