Preheat the oven to 350 degrees, and grease the sections of a mini muffin tray well.
Add the almond flour, butter and cream cheese to a mixing bowl, and blend until smooth.
Press the dough into the sections of a mini muffin tray, to form cookie cups.
Sprinkle some of the chopped pecans into each cookie cup.
Add the melted butter, brown sugar substitute and sugar free honey into a pot on the stove over medium low heat. Stir until the mixture is smooth and sugar has melted.
Remove from the heat and let cool for a few minutes.
Whisk in the egg and vanilla until well combined.
Spoon the filling mixture into the cookie cups, filling them about ⅔ of the way full.
Bake for 10-15 minutes, or until the cookie cups are browned and cooked through.
Let the cookie cups cool to room temperature before serving.