Preheat the oven to 325 degrees, and spray a 9x13 baking dish with baking spray.
In a mixing bowl, combine the almond flour, protein powder, vanilla, eggs, cocoa powder, baking powder, baking soda, 1 cup of the Swerve, almond milk and half of the melted butter. Blend until smooth and fluffy.
Mix together the coconut flakes and pecans in the bottom of the baking dish.
Spread the cake batter over the coconut and pecans.
In a bowl, beat together the remaining butter, cream cheese and ⅓ cup of Swerve until smooth and creamy.
Drop spoonfuls of the cream cheese mixture on the cake, and use the top of a knife or tines of a fork to swirl it into the batter.
Top the cake with the chocolate chips and bake for 45-50 minutes until cooked through.
Let cool before serving.