Preheat oven to 350°F and line a large baking sheet with parchment paper.
Rinse and drain the black beans thoroughly in a fine-mesh sieve to ensure a neutral flavor base.
Place the rinsed beans, almond butter, olive oil, honey, Greek yogurt, and vanilla extract into a food processor.
Process the mixture on high until it is completely smooth and no visible bean skins remain.
Add the almond flour, whey protein isolate, cacao powder, baking powder, and sea salt to the processor.
Pulse the ingredients until just combined into a thick, dark chocolate dough.
Scoop the dough into 25 equal portions and arrange them on the prepared baking sheet.
Gently flatten each cookie with the back of a spoon or damp fingers as they will not spread much during baking.
Bake for 12 to 15 minutes until the edges are firm to the touch but the centers remain slightly soft.
Remove from the oven and allow the cookies to cool completely on the pan to reach their final fudgy texture.