Whisk all-purpose flour, whole-wheat flour, baking powder, baking soda and salt together in a medium bowl. Beat sugar and butter in the bowl of a stand mixer fitted with a paddle attachment on medium speed until creamed, about 90 seconds. Add egg, lemon zest and lemon juice; beat on medium speed until combined, about 1 minute, scraping down the sides of the bowl as needed. With the mixer running on low speed, gradually add the flour mixture, beating until combined, about 1 minute. Cover and refrigerate until slightly firmer, about 30 minutes.

Position racks in lower and upper thirds of oven; preheat to 350°F. Line 3 rimmed baking sheets with parchment paper.

Place confectioners' sugar in a small bowl. Scoop the dough with a 1-tablespoon cookie scoop; roll to create a ball. Roll each ball, one at a time, in the sugar until completely covered. Gently place on a prepared baking sheet. Repeat with the remaining dough, spacing the balls 2 inches apart.

Place 2 of the baking sheets on separate racks; bake until the edges of the cookies are set, about 10 minutes. Let the cookies cool on the pans for 5 minutes, then transfer to wire racks to cool completely, about 15 minutes. Repeat with the remaining sheet of cookies.