In a medium-sized bowl, add 2 cups all-purpose flour, 1/4 cup Hershey's cocoa powder, 1 teaspoon baking soda, and 1/2 teaspoon salt. Whisk to combine, then set aside.
In the large bowl of a stand mixer fitted with the paddle attachment, add 1/2 cup unsalted butter, room temperature, 1/2 cup granulated sugar and 1/2 cup light brown sugar. Beat on medium high speed until light and fluffy.
Add 1 large egg, room temperature and 1 teaspoon vanilla extract and beat on high speed until combined, scraping down the mixing bowl as needed.
In a small bowl, add 1/2 cup whole milk, 1/4 cup sour cream, 1 teaspoon white vinegar and 1 teaspoon red gel food coloring. Whisk to combine.
Add the milk mixture to the batter and beat on a medium speed until combined and uniform in color. The batter may look split at this stage, which is fine.
With the mixer on its lowest speed, gradually add the flour mixture. Beat until you can no longer see streaks of flour, taking care not to over mix.
Transfer the batter to a piping bag fitted with a large round nozzle and refrigerate for one hour. When ready, preheat the oven to 350 degrees F and prepare two large baking sheets with parchment paper.
When the batter has chilled, pipe 1 1/2 inch rounds onto the baking sheets, spacing them a couple of inches apart.
Bake for 10-12 minutes, until set and domed. The tops should spring back lightly when touched.
Remove from the oven and leave on the baking sheets to cool for 5 minutes before transferring to a wire rack to cool completely.
Make the cream cheese filling:
To the large bowl of a stand mixer fitted with the paddle attachment, add 4 ounces full-fat cream cheese, room temperature and 1/4 cup unsalted butter, room temperature. Beat for 1-2 minutes or until smooth and creamy.
Sift 1 1/2 cups powdered sugar into the mixing bowl and add 1 teaspoon vanilla extract and a pinch of salt. Beat on a low speed until incorporated, then increase to medium speed and beat for 3 minutes, or until smooth and fluffy.
Transfer the cream cheese frosting to a piping bag fitted with a star nozzle.
Do your best to match up the red velvet cookies according to size then pipe filling onto the flat side of half of them and sandwich together.
Notes
You can use 3/4 cup buttermilk in place of the milk-and-sour cream mixture if you prefer. We tested both methods, the first with buttermilk, and the second using whole milk and sour cream when we ran out. Surprisingly, the sour cream version produced whoopie pies with a cleaner shape and a softer, slightly richer crumb. Both work well, so choose based on what you have and your preferred texture.
The key to achieving beautifully rounded whoopie pies with a soft, tender crumb is to mix gently and avoid overworking the batter. Chilling the batter briefly helps the cakes hold their shape and achieve that signature dome. A small step that makes a big difference in appearance. Parchment paper promotes the right amount of rise and setting; silicone mats tend to cause them to spread more.
Expect a thick, velvety batter that pipes easily but isn’t stiff like cookie dough.
Because whoopie pies are essentially mini cakes, piping rather than scooping yields a consistent shape and the signature soft, domed finish.
For larger bakery-sized whoopee pies, pipe them to about 2 inches. Or for mini versions, make them 1 inch.
Whoopie pies should stay soft. Overbaking makes them dry quickly. The tops should spring back when lightly touched, and the cakes should look matte, not shiny.
For the filling, over-mixing the cream cheese causes it to loosen, so stop mixing as soon as it looks smooth. If the frosting is too thick and not pipeable, add a tablespoon of heavy cream or milk. Conversely, if it is too thin, add extra powdered sugar a quarter cup at a time. If the filling becomes soft, a brief chill will restore its perfect piping consistency.
Pair similar-sized rounds together before piping the filling; it makes the finished sandwiches look polished and uniform.