Prep your pan and oven. Line a 12-cup muffin tin with paper liners and preheat the oven to 350°F (175°C).
Lightly mist the liners with oil if they tend to stick.
Mix the dry ingredients. In a large bowl, whisk together 2 cups almond flour, 2 tablespoons coconut flour, 1/2 cup granulated keto sweetener, 1 teaspoon baking powder, and 1/4 teaspoon sea salt. Stir in 1/2 cup unsweetened shredded coconut.
Combine the wet ingredients. In a separate bowl, whisk 3 large eggs, 1/2 cup full-fat coconut milk (or heavy cream), 1/3 cup melted coconut oil (or butter), and 1 teaspoon vanilla. Add 1/4 teaspoon coconut extract if you want a bolder coconut note.
Bring it together. Pour the wet mixture into the dry and fold gently until just combined.
The batter will be thick but scoopable. If it’s too dry, add 1–2 tablespoons more coconut milk.
Add chocolate chips. Fold in 1/2 to 2/3 cup sugar-free chocolate chips, reserving a few for the tops.
Fill the liners. Divide the batter evenly among the 12 cups, filling each about 3/4 full. Press a few extra chips on top for looks.
Bake. Bake for 18–22 minutes, or until the tops are set and a toothpick comes out mostly clean with a few moist crumbs.
Avoid overbaking to keep them moist.
Cool. Let the muffins cool in the pan for 10 minutes, then transfer to a rack to cool completely. They firm up as they cool.