Preheat the oven to 325°F and line a standard 12-cup muffin pan with paper or parchment liners.
In a medium bowl, combine the almond flour, melted coconut oil, 1 tablespoon allulose, and sea salt. Stir until the mixture resembles damp sand and holds together when pressed.
Divide the crust mixture evenly between the 12 liners. Press firmly into the bottoms using the back of a spoon or a small flat-bottomed glass.
Bake the crusts for 5–7 minutes, just until fragrant and lightly set. Remove from the oven and allow them to cool slightly.
Slice the vanilla bean lengthwise and scrape out the seeds. Set the seeds aside. If using vanilla extract instead, reserve it for the filling.
Place the softened cream cheese in a large mixing bowl and beat on medium speed until completely smooth, scraping down the sides of the bowl as needed.
Add the Greek yogurt and ½ cup allulose. Mix on low to medium speed just until smooth and combined, avoiding excessive whipping.
Add the eggs one at a time, mixing gently after each addition until incorporated.
Add the vanilla bean seeds, lemon zest, lemon juice, and cinnamon. Mix gently until the flavorings are evenly distributed throughout the batter.
Divide the cheesecake mixture evenly among the prepared muffin cups, filling each approximately three-quarters full. Gently tap the pan once or twice against the counter to release large air bubbles.
Bake for 20–25 minutes, or until the edges are set and the centers still have a slight gentle wobble. Do not wait for the centers to become completely firm.
Remove the pan from the oven and cool the cheesecakes in the pan for 20–30 minutes. Transfer them to the refrigerator and chill for at least 4 hours, preferably overnight.
When completely chilled, sprinkle a very thin, even layer of allulose over each cheesecake.
Using a kitchen torch, caramelize the allulose while continuously moving the flame across the surface. Stop when the topping is melted, golden, and crisp.
Allow the brûlée topping to cool for 1–2 minutes so it hardens into a delicate shell.
Serve the cheesecake cupcakes cold, optionally garnished with fresh berries, lemon zest, mint, or a light sprinkle of cinnamon.