Preheat your oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners. Lightly mist the liners with oil to prevent sticking.
Make the cream cheese swirl: In a small bowl, beat cream cheese, egg yolk, powdered sweetener, and vanilla until smooth and creamy.
Set aside.
Mix dry ingredients: In a large bowl, whisk almond flour, cocoa powder, coconut flour, baking powder, baking soda, and salt until combined and lump-free.
Whisk wet ingredients: In a separate bowl or large measuring cup, whisk eggs, almond milk, oil (or butter), vanilla, and granulated sweetener until the sweetener starts to dissolve.
Combine: Pour the wet mixture into the dry. Stir gently until just combined. If using, fold in sugar-free chocolate chips and espresso powder.
Portion batter: Divide the chocolate batter evenly among the muffin cups, filling each about two-thirds full.
Add the swirl: Spoon about 1 tablespoon of the cream cheese mixture into the center of each cup.
Use a toothpick or skewer to swirl it lightly into the batter.
Bake: Place the pan on the center rack and bake for 18–22 minutes. The muffins are done when the tops spring back lightly and a toothpick inserted into the chocolate portion comes out with a few moist crumbs.
Cool: Let the muffins cool in the pan for 10 minutes, then transfer to a wire rack. Cool completely before storing so the cream cheese sets.
Enjoy: Serve slightly warm or at room temperature.
The flavors deepen after a few hours.