Set the oven rack to the center position and preheat to 180 Celsius / 350 Fahrenheit. Line an 8-cup muffin pan with parchment liners or prepare a flexible silicone tray.

Beat the room-temperature eggs with an electric mixer or blender for about 2 minutes. Stop once the mixture becomes pale, frothy, and noticeably thicker in volume.

Pour the yogurt, melted butter, almond milk, and vanilla extract into the whipped eggs. Mix briefly until the liquids are fully emulsified without deflating the egg foam.

Add the almond flour, coconut flour, baking powder, granulated sweetener, and cocoa powder. Stir gently until a thick, glossy chocolate batter forms and no dry pockets remain.

Fold most of the sugar-free chocolate chips into the batter, setting a small spoonful aside. Distribute the chips evenly throughout the mixture using a soft spatula.

Divide the batter among the 8 prepared muffin cups and press the reserved chips onto the tops. Fill each cup nearly to the top to encourage tall, rounded muffin domes.

Bake for 22 to 25 minutes until the centers are set and spring back gently to the touch. Cool the pan on a heat-safe surface for 10 minutes before moving the muffins to a wire rack.