Preheat the oven to 350 degrees F and line a mini cupcake pan with papers. In a large bowl, combine the flours, sugar, baking powder, baking soda, salt, and lemon zest.
Add the softened butter and mix on low speed until the mixture resembles coarse crumbs.
Add the eggs, one at a time, scraping the sides and bottom of the bowl after each addition.
Add the yogurt, vanilla, and lemon juice, mix for 30 seconds, and scrape the bowl again. Mix for another minute.
Fill the cupcake liners about ½ to ⅔ full. (Be careful not to overfill, the cupcakes will puff up a lot as they bake.)
Bake for 12-14 minutes, or until the mini cupcakes are springy to the touch, and a toothpick inserted in the center comes out clean or with one or two moist crumbs. (Regular sized cupcakes will need about 18-20 minutes bake time.)
Cool completely before frosting.