Preheat your oven to 180°C (350°F).
Line a muffin tin with cupcake liners or lightly grease each cup with coconut oil.
In a large mixing bowl, combine the unsweetened applesauce, creamy peanut butter, honey, eggs, melted coconut oil, and water. Blend until smooth.
In another bowl, whisk together the whole wheat flour and baking powder.
Gradually add the dry ingredients to the wet mixture, mixing until just combined.
Spoon the batter into the prepared muffin tin, filling each cup about two-thirds full.
Bake for 20-25 minutes or until a toothpick inserted in the center comes out clean.
Let the cupcakes cool in the tin for about 5 minutes, then transfer them to a cooling rack.
Prepare the frosting by beating the cream cheese and peanut butter together until smooth.
Frost the cooled cupcakes generously with the peanut butter cream cheese frosting.
Optionally, place a small milk bone on top of each cupcake.