Preheat your oven to 350°F (175°C).
Prepare a muffin tin by lining with cupcake liners or greasing it well.
In a medium bowl, whisk together flour, cocoa powder, and salt.
In a separate mixing bowl, combine melted butter and granulated sugar until well blended.
Add the eggs and vanilla extract to the butter mixture, whisking until fully incorporated.
Gradually mix in the dry ingredients until just combined; do not overmix.
Divide the brownie batter evenly into the prepared muffin tin, filling each cup about halfway.
In another bowl, beat together the softened cream cheese, powdered sugar, lemon juice, and vanilla until smooth.
Spoon the cheesecake batter on top of the brownie batter in each cup, filling them nearly to the top.
Sprinkle chocolate chips on top of the cheesecake layer, if using.
Bake in the preheated oven for about 20-25 minutes, or until the tops are slightly set.
Allow the cups to cool in the pan for 10 minutes before transferring to a wire rack.
Once cooled, top with whipped cream and any additional toppings before serving.