Preheat the oven to 350F. Coat a 24-cup mini muffin tin with cooking spray.
In the bowl of an electric stand mixer fitted with the paddle attachment (or large bowl with a hand mixer), beat together the softened butter, peanut butter, and brown sugar until smooth and well incorporated, about 1-2 minutes on speed medium. Next, mix in the eggs and vanilla extract until smooth. Finally, add in the flour, cocoa, baking soda, and kosher salt then mix until well combined.
Using a small cookie scoop, fill all 24 mini muffin cups with the batter (each hole will be filled to top). Sprinkle 3-4 chocolate chips on top of each muffin batter then sprinkle flaky sea salt over top of all of the mini muffins.
Bake in the oven until a toothpick inserted into the center of one muffin comes out clean, about 13-15 minutes.
Allow to cool before enjoying as the chocolate chips on top of mini muffins will be quite gooey. Store in the fridge for up to 5 days :)