Line a standard 12-cup muffin tin with paper liners. Divide the crust mixture among the liners, using approximately 2 tablespoons per cup. Press firmly into the bottom of each liner. Refrigerate for 15–30 minutes while you prepare the filling.

In a large mixing bowl, beat the softened cream cheese until smooth. Add the sweetened condensed milk, brown sugar, vanilla extract, lemon juice, cinnamon, ginger, and nutmeg. Mix until smooth and thoroughly combined.

Spoon approximately 2 tablespoons of filling over each chilled crust, dividing the filling evenly among the 12 cups. Smooth the tops. Refrigerate for at least 5 hours, or overnight, until set.

While the cheesecakes chill, prepare the candied pecans. Melt the butter in a saucepan over medium-low heat. Add the pecans and stir for 2 minutes. Add the brown sugar and continue stirring until it melts and coats the pecans. Transfer to a parchment-lined plate and cool completely, then break into small pieces.

Keep the cheesecakes refrigerated until ready to serve. Carefully remove the paper liners, if desired, and top with the cooled candied pecans just before serving.