Step 1: If eggs are cold, place them in a bowl of warm water for about 10 minutes to bring to room temperature. In a stand mixer (or large bowl with hand mixer), beat the room temperature eggs and granulated sugar on medium-high speed for 3 to 4 minutes, until pale, thick, and fluffy.
Step 2: In a microwave-safe bowl, combine chocolate chips and butter. Heat in 30-second bursts, stirring after each, until completely melted and smooth. Stir in instant coffee or espresso powder (if using). Let the mixture cool slightly for 2-3 minutes.
Step 3: Add vanilla extract to the whipped egg and sugar mixture and mix briefly. Slowly pour the slightly cooled melted chocolate mixture into the egg mixture. Gently fold with a spatula until fully incorporated and glossy.
Step 4: Stir in the salt and baking powder. Sift the cocoa powder and flour over the batter. Gently fold the dry ingredients into the wet mixture with a spatula just until no dry streaks remain. Do not overmix.
Step 5: Cover the bowl and let the dough rest at room temperature for about 30 minutes to hydrate the flour and firm up slightly.
Step 6: While the dough rests, preheat oven to 350°F (175°C) and line baking sheets with parchment paper.
Step 7: Use a 1.5-tablespoon cookie scoop to portion dough onto prepared baking sheets, leaving space between cookies (about 8 per sheet). Spoon small amounts of runny natural peanut butter over the top of each dough ball. Use a toothpick or chopstick to gently swirl the peanut butter into the surface of the dough.
Step 8: Bake for 5 to 6 minutes, until the edges look set but the centers still look a little soft or slightly underdone. Do not overbake.
Step 9: Immediately remove baking sheets from the oven. If needed, gently nudge the edges of the warm cookies with the back of a spoon to shape them into a nice round. Let cookies cool on the baking sheet for about 2 minutes before transferring to a wire rack to cool completely.