Preheat your oven to 350 degrees F (175 degrees C). This is an essential first step, as a properly preheated oven ensures that your cookies bake evenly and achieve that perfect texture. While the oven is heating, line a baking sheet with parchment paper or a silicone mat to prevent sticking.
In a large bowl, sift together flour, cocoa powder, chipotle, baking powder, baking soda, and salt. Sifting is key here—it aerates the ingredients and helps prevent clumping. Set this mixture aside while you prepare the wet ingredients.
In another large mixing bowl or the bowl of a stand mixer, combine butter, brown sugar, and granulated sugar. Beat them together until the mixture is the consistency of wet sand with no visible chunks of butter. This step is vital to create a smooth texture.
Add in the eggs, one at a time, mixing well after each addition. This process adds air to the batter, which will help the cookies rise. Also, mix in the vanilla until fully incorporated.
Gradually add the dry ingredients to the wet mixture, mixing on low speed until everything is just combined. Be careful not to overmix; you want a soft dough that holds together well.
Once combined, gently fold in the mini chocolate chips with a spatula or spoon. This will ensure that there are chocolatey pockets of goodness in each cookie.
Using a cookie scoop or a heaping tablespoon, drop the dough onto the prepared baking sheet, leaving an inch or two of space between each scoop. The cookies will spread as they bake, so give them room!
Bake for 10 to 12 minutes or until the centers are set. You'll know they're done when the edges look firm, and the tops may have a slight sheen.
Let them cool on the baking sheet for 2 minutes before transferring them to a wire cooling rack. This allows them to set a bit more without falling apart.
Once completely cool, store your Double Chocolate Chipotle Cookies in an airtight container for up to 3 days. You can also enjoy them warm for that freshly-baked flavor!