Prepare your equipment and ingredients. Preheat your oven to 325°F (165°C) and line a 24-cup mini muffin tin with paper liners. Set out cream cheese to soften if you haven’t already.
Make the graham cracker crust. In a food processor, combine graham cracker crumbs, melted butter, sugar, and salt. Pulse until the mixture resembles wet sand and holds together when pressed between your fingers.
Form the mini crusts. Place about 1 teaspoon of the graham cracker mixture into each muffin cup and press down firmly using the back of a measuring teaspoon or your fingers to create a compact base.
Pre-bake the crusts for 5 minutes until just set, then remove from the oven and let cool while preparing the filling. Keep the oven on.
Beat the cream cheese and sugar in a large bowl using an electric mixer on medium speed until smooth and fluffy, about 2 minutes. Scrape down the sides of the bowl to ensure even mixing.
Add the egg and vanilla to the cream cheese mixture and beat on low speed until just combined. Overbeating after adding the egg can cause the cheesecakes to crack.
Fold in the sour cream and flour using a rubber spatula until completely incorporated and the mixture is smooth.
Fill each muffin cup with the cheesecake batter, filling each about ¾ full. A small cookie scoop works perfectly for this task.
Bake the cheesecake bites for 12-15 minutes or until the centers are almost set (they should still have a slight jiggle).
Cool the cheesecakes completely in the pan on a wire rack for 30 minutes, then transfer to the refrigerator to chill for at least 2 hours.
Prepare the topping by mixing together the chopped cranberries, pistachios, honey, and orange zest (if using) in a small bowl.
Top each chilled cheesecake bite with a small spoonful of the cranberry-pistachio mixture, gently pressing it into the surface so it adheres.
Return to the refrigerator for another 30 minutes to set the topping before serving.