Prep the pan: Preheat your oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or grease well.
Mix dry ingredients: In a large bowl, whisk together almond flour, cocoa powder, sweetener, baking powder, baking soda, and salt, breaking up any clumps.
Combine wet ingredients: In a separate bowl, whisk eggs, yogurt, almond milk, melted butter, vanilla, and optional coffee until smooth.
Bring it together: Pour wet mixture into dry.
Stir with a spatula until just combined. The batter will be thick but scoopable. Fold in chocolate chips.
Portion: Divide the batter evenly among the muffin cups.
Sprinkle a few extra chips on top for a bakery look.
Bake: Bake for 18–22 minutes, until the tops are set and a toothpick inserted in the center comes out with a few moist crumbs.
Cool: Let muffins cool in the pan for 5 minutes, then transfer to a rack to cool completely. They firm up as they cool.
Serve: Enjoy warm or at room temperature. For maximum gooey chips, rewarm for 10–15 seconds in the microwave.