Preheat the oven to 350°F (175°C). Line a standard 12-cup muffin tin with silicone liners or grease with coconut oil.
In a medium bowl, combine almond flour, 2 tbsp maple syrup, 2 tbsp melted coconut oil, 1 tsp vanilla, and salt. Stir until a cohesive dough forms.
Divide the dough into 12 equal portions and press firmly into the bottom of each muffin cup to create a flat, even base.
Bake for 10 to 12 minutes or until the edges are lightly golden. Remove from the oven and allow to cool completely in the tin.
Prepare the caramel by whisking together almond butter, 1/4 cup maple syrup, 2 tbsp melted coconut oil, 1 tsp vanilla, and a pinch of salt until smooth and emulsified.
Spoon the caramel mixture evenly over the cooled cookie bases. Place the tin in the freezer for 30 minutes to set the caramel layer.
Melt the chocolate chips and 1 tbsp coconut oil together using a double boiler or a microwave in 30-second intervals, stirring until smooth.
Pour the melted chocolate over the frozen caramel layer in each cup. Gently tap the tin on the counter to smooth the surface.
Sprinkle with flaky sea salt while the chocolate is still wet.
Chill in the refrigerator for at least 30 minutes or until the chocolate is fully set. Serve chilled and store in an airtight container in the refrigerator.