Prep the pan. Heat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or lightly grease with oil.
Mix dry ingredients. In a large bowl, whisk together the almond flour, tapioca flour, baking powder, baking soda, and salt until no lumps remain.
Whisk wet ingredients. In a separate bowl or measuring cup, whisk the eggs, maple syrup, milk, oil, and vanilla (plus almond extract if using) until smooth and well combined.
Combine. Pour the wet mixture into the dry and whisk until just blended.
The batter will be thicker than classic muffin batter but still scoopable.
Fold in chocolate. Stir in the chocolate chips with a spatula, keeping a few aside to sprinkle on top.
Portion. Divide the batter evenly among the muffin cups, filling each about 3/4 full. Add the reserved chocolate chips on top.
Bake. Bake for 18–22 minutes, or until the tops are set and lightly golden and a toothpick inserted in the center comes out mostly clean with a few moist crumbs.
Cool. Let the muffins cool in the pan for 5 minutes, then transfer to a wire rack to cool completely. This helps them set and prevents soggy bottoms.