Preheat your oven to 350°F (177°C). Line a 12-cup muffin tin with cupcake liners.
In a medium bowl, whisk together the all-purpose flour, cocoa powder, baking soda, baking powder, and salt.
In a large bowl, beat the eggs, applesauce, melted coconut oil, Greek yogurt, milk, brown sugar, and vanilla extract until smooth.
Gradually add the dry ingredients to the wet ingredients, mixing until just combined. Be careful not to overmix.
Divide the batter evenly among the cupcake liners, filling each about ⅔ full. Bake for 18-20 minutes until the cupcakes spring back when gently touched.
Let the cupcakes cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.
In a large bowl, beat the softened butter and peanut butter together until creamy and smooth.
Gradually add the powdered sweetener, mixing well after each addition.
Add the heavy cream and vanilla extract, and beat until the frosting is smooth and fluffy. If the frosting is too thick, you can add an extra tablespoon of cream or milk to reach your desired consistency.
Once the cupcakes are completely cool, spread or pipe the frosting on top of each one.