Preheat the oven to 350 degrees Fahrenheit and prepare a muffin baking pan by spraying it with cooking spray. Set it aside for now.
Combine the all-purpose flour, graham cracker crumbs, baking powder, cinnamon, and nutmeg into a bowl and whisk together until combined.
With a standing or hand mixer, beat together the salted butter, granulated white sugar, and light brown sugar until the consistency turns light and fluffy, about 1-3 minutes.
Beat in the egg and vanilla extract.
Stir in the flour mixture until just combined. Do not overmix. The dough should be a little crumbly.
Evenly fill each muffin tin with the batter completely to the top.
Bake in the oven for 20-25 minutes or until golden brown and the top is set.
Once the cookies come out of the oven, immediately use a tablespoon to push indents into the center of each cookie to make room for the marshmallow. Fill each indent with one marshmallow half.
Bake the cookie cups in the oven for 2 more minutes. If you would like to brown the tops, broil for 1 minute or until golden brown. Keep a close eye because it can burn very quickly.
Let the cookies sit for a few minutes before topping with one piece of the Hershey’s chocolate bar. Plate and serve.