Preheat the oven to 350°F. Line a 9x9 square baking pan with a parchment sling and set aside.
In a medium bowl, add the melted ghee, almond butter, maple syrup, coconut sugar, and egg. Whisk to combine until thick and smooth, about 1 minute. Add the vanilla and whisk once more to combine.
In a medium bowl, add the almond flour, tapioca, baking soda, baking powder, salt, and cinnamon. Whisk to combine.
Add the dry ingredients to the wet, stirring with a wooden spoon until just combined. The mixture should be thick, between a brownie batter and a cookie dough.
Using a sharp knife, roughly chop the cookies until they resemble a crumble texture. You don’t want them be superfine crumbs or the bars will turn out dry. Add to a small bowl and toss with the chopped chocolate. Add ¾ of the chocolate/graham mixture to the dough along with ¾ cup of the mini marshmallows. Fold the mix-ins into the dough until evenly distributed.
Transfer the dough into the prepared baking pan, using the back of a spoon to press into an even layer. Top with the remaining chocolate and graham mixture.
Transfer to the oven and bake on the middle rack for 16 minutes. Remove from the oven and top with the remaining marshmallows.
Transfer back to the oven and bake for an additional 6 to 9 minutes (22 to 25 minutes in total), or until a toothpick comes out clean when poked in the center of the bars.
Sprinkle with flaky salt. Allow to cool entirely before cutting into 16 squares. Enjoy!