With a small cookie scoop or spoon, scoop the dough by tablespoonfuls and roll into a ball. Place 2 inches apart on the prepared baking sheet. With your fingers, lightly press the cookie balls to a 1/4-inch thickness. If the dough is sticky, dampen your fingers slightly.
In the bowl of a standing mixer fitted with the paddle attachment or a large mixing bowl, cream together the butter, sugar, and cream cheese until light and fluffy, about 3 full minutes, stopping to scrape down the bowl as needed. Beat in the vanilla extract, lemon zest, and egg, stopping to scrape down the bowl again. With the mixer running on low speed, slowly add the flour mixture, beating just until incorporated.
Preheat the oven to 375 degrees F. Line two baking sheets with parchment paper or a silpat mat . In a medium mixing bowl, whisk together the whole wheat pastry flour, baking powder, baking soda, and salt. Set aside.