Preheat the oven to 350°F (175°C). Line a 12-cavity muffin pan with 9 liners and pour water into the remaining three cavities halfway up the sides to create a water bath for even baking.
Make the crust: Pulse the graham cracker sheets in a food processor until fine crumbs remain. Transfer to a bowl and stir in 1 tablespoon granulated sugar and the melted butter until evenly moistened.
Divide the crumb mixture evenly among the 9 prepared liners and press firmly into the bottoms using a milk cap or the back of a tablespoon to form compact crusts.
Prepare the filling: In a medium bowl, beat the room-temperature cream cheese and 1/2 cup granulated sugar at low speed until smooth and creamy. Add the flour, vanilla extract, egg, lemon zest (1/2 tablespoon), and 2 tablespoons lemon juice, then beat until just combined and smooth.
Divide the cheesecake batter evenly among the 9 crust-lined cups, smoothing the tops slightly. Bake in the preheated oven for 22–27 minutes, until the edges are set and the centers still jiggle slightly.
Cool the cheesecakes at room temperature for 30 minutes, then transfer to the refrigerator and chill for at least 2 hours; the centers may sink a bit as they cool.
Heat part of the jam: Place 4 1/2 tablespoons of blueberry jam in a small microwave-safe bowl and warm for 10–15 seconds until spreadable. Spoon about 1/2 tablespoon of jam onto each chilled cheesecake and spread to cover the top.
Top each cheesecake with 4–6 fresh blueberries, depending on size.
Place the remaining 1 1/2 tablespoons jam in the microwave-safe bowl and warm for 10–15 seconds. Brush the warm jam over the fresh blueberries to glaze them. Dust with powdered sugar if desired.