In a medium bowl, whisk together the flour, baking powder, baking soda, and salt. Set aside.

In a large bowl using a hand mixer or a stand mixer fitted with a paddle attachment, beat the butter, granulated sugar, and brown sugar together on medium-high speed until creamed, about 3 minutes. (Here’s a helpful tutorial if you need guidance on how to cream butter and sugar.) Add the egg, egg yolk, and vanilla extract, and beat on medium-high speed until combined. Scrape down the sides and bottom of the bowl as needed.

Add the dry ingredients to the wet ingredients and beat on low speed until incorporated, then increase to medium-high speed and beat until fully combined. The dough will be thick. Divide it into 3 equal portions.

Return one portion of dough to the mixing bowl. Add the chopped, blotted cherries, 3 Tablespoons flour, and pink gel food coloring (if using). Beat on medium speed until combined. Transfer the cherry dough to a bowl and refrigerate it while you prepare the remaining 2 doughs. Wipe the mixer bowl clean.

Return another portion of dough to the mixing bowl. Add the ground pistachios, almond extract, and green gel food coloring (if using). Beat on medium speed until combined. Set aside. Wipe the mixer bowl clean.

Return the final portion of dough to the mixing bowl. Add the cocoa powder, cherry juice, and mini chocolate chips. Beat on medium speed until combined. Set aside.

Line baking sheets or large plates with parchment paper. Remove the cherry dough from the refrigerator. Scoop and roll it into small balls, about 15g each (a heaping 1/2 Tablespoon). Place on the lined baking sheet or plate, then refrigerate these cherry dough balls while you shape the pistachio and chocolate doughs. Repeat the shaping process with the pistachio and chocolate doughs, rolling all remaining dough into small balls, about 15g each.

Place the granulated sugar for rolling in a small bowl or on a plate. Remove the cherry dough balls from the refrigerator/freezer. Press together 3 dough balls—1 of each flavor—and roll them into a single 45g cookie dough ball. Roll each marbled dough ball in the granulated sugar, then place on a lined baking sheet. Once all cookies are shaped and coated, cover and refrigerate the dough balls for at least 1 hour before baking (or up to 3 days). Chilling the shaped dough balls is imperative.

Preheat oven to 350°F (177°C). Line large baking sheets with parchment paper or silicone baking mats. Arrange the chilled cookie dough balls 3 inches apart on the lined sheets, about 8 or 9 cookies per sheet.

Bake until the edges are set but the centers still look soft, about 14–16 minutes. Allow cookies to cool on the baking sheet for 5 minutes, then transfer to a wire rack to cool completely.

Store cookies in an airtight container at room temperature for up to 5 days.