Preheat your oven to 325°F and prepare a cookie sheet by lining it with parchment paper. This ensures the cookies don’t stick and helps with even baking.
In a large bowl, combine butter and brown sugar. Using an electric mixer, beat on medium speed until the mixture turns light and fluffy. This usually takes about 2 to 3 minutes, and you’ll notice the color change.
Add in the egg and vanilla. Beat until well blended, ensuring the egg is fully incorporated into the mixture.
Next, add the flour, graham cracker crumbs, and salt. Mix on low speed for about a minute. Be careful not to over-mix; you want a stiff dough that holds its shape.
Shape the dough into balls, using about a heaping teaspoon for each. Place them on the prepared cookie sheet with at least 2 inches between each cookie to allow for spreading.
With your thumb or the back of a spoon, create an indentation in the center of each ball. This is where the magic will happen with the marshmallows and chocolate.
Bake the cookies in the preheated oven for 8 to 10 minutes. Watch for the edges to turn slightly golden and the cookies to firm up.
After baking, remove the cookies from the oven and immediately press 2 miniature marshmallows into the center of each cookie. Return the tray to the oven for an additional 2 to 3 minutes, just until the marshmallows are melted.
Once out of the oven, let the cookies cool for about 2 to 3 minutes. Then, top each marshmallow with a rectangle of milk chocolate. Let it sit until the chocolate melts, and you can spread it gently over the marshmallow with the back of a spoon.
Allow the cookies to cool completely on the baking sheet, letting the chocolate set before transferring them to a wire rack. Enjoy your freshly baked S'mores Thumbprints with a glass of milk or coffee!