Preheat the oven to 350°F (180°C) and grease mini muffin pans liberally with cooking spray.
In a medium bowl, whisk together the flour, cocoa powder, baking powder, and salt until combined, then set aside.
Place the butter and chopped chocolate in a heatproof bowl and melt in your microwave for about 1 minute. Stir and continue to melt in 30 second bursts until smooth. Set aside to cool.
In the bowl of a stand mixer fitted with the whisk attachment or in a large bowl using an electric hand mixer, whisk together the eggs, sugars, and vanilla for 5-6 minutes on medium-high speed.
With the mixer on, pour in the slightly cooled chocolate mixture and mix until smooth. Sift in the dry ingredients and use a rubber spatula to gently fold until just combined.
Using a 1.5-tbsp cookie scoop (#40), drop dough into mini muffin pan.
Bake for about 15-20 minutes. The brownies will be soft but set around the edge. Allow them to cool in the muffin pan for a few minutes and then use the back of a tsp to create a indent in the middle of the brownie (so they look like cups) Allow the brownie cups at least 15 minutes to cool before removing from the tray to cool completely.