How to Make It
Prepare the Chocolate Sugar Cookie Dough: Beat butter and sugar with a heavy-duty electric stand mixer on medium-high speed until light and fluffy, about 3 minutes. Add eggs and vanilla. Beat on medium until combined, stopping to scrape down sides of bowl as needed.
Stir together flour, cocoa, baking powder, and salt in a medium bowl. With mixer running on low speed, add flour mixture to butter mixture, beating until just incorporated.
Shape dough into a disk, wrap tightly in plastic wrap, and chill at least 2 hours or up to 2 days.
Prepare the Cookie Cups: Divide dough into 40 (1-Tbsp.) balls. Place 1 ball in the cups of 2 (24-cup) lightly greased miniature muffin pans. (You’ll fill only 40 cups.) Using a teaspoon measure, press dough into bottom and up sides of muffin cups. Chill 20 minutes.
Preheat oven to 350°F. Bake in preheated oven until cookies are dry to the touch and shape is set, about 10 minutes. Immediately press cookies again with teaspoon. Cool cookie cups in pans on a wire rack 5 minutes. Transfer cookie cups to wire rack to cool completely, about 30 minutes.
Meanwhile, beat butter, cream cheese, and 2 tablespoons jarred caramel sauce with a heavy-duty electric stand mixer on medium speed until creamy, 1 to 2 minutes. Reduce speed to low, and, with mixer running, gradually add powdered sugar, beating until smooth. Beat in vanilla extract and flaky sea salt.
Transfer filling to a piping bag fitted with a large star tip, and evenly pipe into cooled cookie cups. Drizzle about 1 tsp. jarred caramel sauce on each filled cookie cup. Sprinkle each cookie with desired amount of flaky sea salt, and top each with a toasted pecan half.