Preheat the oven to 350°F. Spray muffin tins with nonstick cooking spray.

In the bowl of a stand mixer, combine the light brown sugar, granulated sugar, and butter until well incorporated. Add vanilla extract and eggs, and mix until combined.

In a separate bowl, sift together the flour, baking soda, and kosher salt.

Gradually add the flour mixture to the sugar mixture, mixing until well combined.

Using a 2-tablespoon scoop, add dough to each muffin cup. Press the dough into the bottom of each cup and up the sides to about halfway.

Bake the cookie cups for 10-12 minutes, or until they turn golden brown.

Remove the cookie cups from the oven. While they are still hot, use a spice jar or a shot glass to press down in the middle of each cup, creating a well.

Let the cookie cups cool as you make the caramel.

In a large saucepan over medium heat, melt butter. Add sweetened condensed milk, heavy cream, corn syrup, brown sugar, salt, and vanilla. Stir until combined.

Continue cooking until the mixture reaches 236°F on a candy thermometer, stirring constantly (about 15-18 minutes).

In a microwave-safe bowl, combine the chocolate chips and heavy cream. Heat in 20-second increments in the microwave, stirring after each, until melted and smooth.

Remove the cooled cookie cups from the muffin tins. Fill each with 1 tablespoon caramel, 1 tablespoon ganache, and ½ teaspoon chopped pecans.

Drizzle with extra caramel and sprinkle with kosher salt.