Preheat your oven to 350°F (175°C).
In a medium bowl, whisk together the all-purpose flour, cocoa powder, baking powder, baking soda, and salt. Set aside.
In a large mixing bowl, beat the softened butter, granulated sugar, and brown sugar together with an electric mixer until light and fluffy, about 2-3 minutes.
Add the eggs, one at a time, mixing well after each addition. Stir in the vanilla extract.
Gradually add the dry ingredients to the wet ingredients, mixing until just combined.
Gently fold in the semi-sweet and milk chocolate chips.
Cover the dough with plastic wrap and refrigerate for at least 30 minutes.
Line baking sheets with parchment paper. Using a cookie scoop, portion out the chilled dough onto the sheets.
Take a small amount of dough, flatten it, place about a teaspoon of Nutella in the center, fold the dough over, and seal it well.
Bake the cookies for 10-12 minutes, or until the edges are set but the centers are still soft. Sprinkle with sea salt immediately if desired.
Allow the cookies to cool on the baking sheet for 5 minutes before transferring them to a wire rack to cool completely.