Preheat your oven to 325 degrees. Line a muffin tin with foil baking cups and grease with cooking spray.
In a medium sauce pan, bring the sugar, water, and butter to a boil. Turn off the heat and mix in the chocolate chips. Stir constantly until the chocolate chips are fully melted and incorporated.
Add the eggs and vanilla extract to the chocolate mixture. Mix until everything is combined and the chocolate mixture is shiny.
In a large bowl, whisk together the flour, salt, and baking soda.
Make a well in the center of the dry mixture and pour in the chocolate mixture.Stir until combined and there are no dry spots.
Fill the muffin cups 3/4 full with the muffin batter.
Bake for 18-20 minutes, until no longer jiggly.
Remove from the oven and set your oven to broil.
Place 4-5 mini marshmallows at the center of each brownie, pressing down gently to ensure they don't fall off.
Place the brownies under the broiler for 15-20 seconds, until the marshmallows begin to brown. Watch them carefully so they don't burn.
Remove from the oven and sprinkle graham cracker pieces over the marshmallows.
Cool in the pan for 10 minutes. Remove the s'mores brownie bites and let cool on a wire rack.