Pre-heat oven to 350 degrees Fahrenheit and line muffin pan with muffin liners.
In a large bowl, add 1½ cup all purpose flour plus 1 tbsp. of all purpose flour. Whisk together with sugar, baking powder, salt, and baking soda.
In another bowl, whisk together melted butter and egg. Then whisk in buttermilk, milk, and the lemon zest. Add the wet ingredients into the bowl of the dry ingredients and stir and mix until all is incorporated.
In a small bowl, toss blueberries with the remaining 1 tbsp. of flour. This ensures that the blueberries won't sink to the bottom of the batter when you add them to the batter.
Add the flour coated blueberries to the batter and gently fold them in until all incorporated.
Using an ice cream scoop, evenly divide batter amongst the 12 muffin cups.
Bake for 25 minutes, or until toothpick inserted in the middle of the cupcakes come out clean. Let cool completely on a wire rack.
In the meantime, while the cupcakes cool, prepare the frosting by beating together, in a stand mixer or using a hand mixer, cream cheese and butter with the lemon zest, vanilla extract, and salt. Gently add in the powdered sugar and the lemon juice. Beat until the frosting has come together.
Once the cupcakes have cooled completely, place frosting in a piping bag and pipe frosting on top of cupcakes. Garnish with three fresh blueberries. Repeat for all cupcakes.