Line a muffin pan with 12 paper liners. Set it aside.
Using a double boiler or microwave, melt the milk chocolate and coconut oil until smooth. Spoon about 2 teaspoons of melted chocolate in each cup. Use a spoon or knife to spread chocolate about halfway up the sides of the liners. Pop into the refrigerator to harden.
Place the pumpkin puree onto a plate. Use paper towel, press down and blot the pumpkin. Do this a few times, until as much liquid is absorbed from the pumpkin puree as possible.
Combine the blotted pumpkin puree, peanut butter, powdered sugar, almond flour, pumpkin pie spice, salt and vanilla extract. Mix until everything is combined a dough forms.
Scoop 12 equal amounts of the peanut butter cookie dough and roll them into balls. Take the chocolate cups out of the refrigerator. Place one ball of cookie dough in each of the chocolate cups.
Using your hands or the bottom of a glass, gently press down the cookie dough to flatten it into an even layer, touching the sides of the chocolate cup.
Re-melt the remaining milk chocolate. Once smooth again, spoon equal amounts of the melted chocolate onto the tops of each peanut butter cups. Spread it evenly to cover the entire cup. There should be just the right amount left to cover all 12 cups. Now that the cups are done, pop them in the refrigerator to set completely.