In a medium bowl, whisk together the flour, baking soda, baking powder, and salt; set aside.
In a large bowl, whisk together the butter, sugar, and lemon zest until smooth. Add the eggs, lemon juice, and vanilla until well combined. Add the flour mixture and mix until smooth.
Cover with plastic wrap and refrigerate for at least 2 hours.
Preheat the oven to 350°F (180°C), or 160°C for a fan oven, and line two half-size sheet pans with parchment paper.
Using a two-tablespoon scoop, scoop the dough into the granulated sugar and roll it to coat. Transfer to the powdered sugar and roll to generously coat with powdered sugar.
Place the sugar-coated cookie dough on the prepared baking sheet 2 inches apart and bake in the preheated oven for 9-11 minutes, or until puffed and the sugar has cracked.
Cool for 5 minutes on the baking sheet before transferring to a wire rack to cool completely
Notes
Chill the Dough: The chilling step is very important in this cookie recipe! We are making the dough with melted butter, and it needs to be chilled again so the dough is easy to work with. Without chilling, this cookie dough is very sticky and will spread too much in the oven.
Don't Overbake: Overbaked crinkle cookies will be dry. The baking time in this recipe is a guide, as everyone's oven may cook a little bit differently. Keep an eye on the cookies and pull them when they are just barely done.
Use a Cookie Scoop: A cookie scoop helps to portion the dough out perfectly so that all of the lemon crinkle cookies are the same size and shape. I'm making these cookies with a 2-tablespoon scoop, but they can be made smaller. Just reduce the baking time as needed.
Bake One Tray at a Time: This recipe works best if each tray of cookies is baked in the very center of the oven, so don't try to bake two trays at once unless you're really pressed for time.
To Store: Keep these cookies in an airtight container at room temperature for 3-5 days or freeze for up to 3 months.