Preheat your oven to 180°C / 350°F. Line a muffin tin with paper liners or grease lightly with coconut oil.
Mix the wet ingredients. In a large bowl, whisk together the eggs, Greek yogurt, brown sugar, and vanilla extract until smooth and well combined.
Add the dry ingredients. Sift in the sweet potato flour, cocoa powder, baking powder, baking powder and salt. Stir until a thick, uniform batter forms. Do not overmix.
Fold in the chocolate chips, reserving a small handful for the tops.
Portion the batter evenly into the muffin cups, filling each about ¾ full. Top each muffin with a few reserved chocolate chips.
Bake for 18–22 minutes, or until a toothpick inserted in the center comes out with just a few moist crumbs (not wet batter). The tops should look set and slightly domed.
Cool in the pan for 5 minutes, then transfer to a wire rack. The muffins firm up as they cool — resist cutting them too early.