Add about 1 tablespoon of crushed granola to the bottom of each cavity in a silicone muffin pan, creating an even layer.
In a medium mixing bowl, combine the Greek yogurt, peanut butter, and vanilla protein powder until the mixture is thick and smooth.
Spoon approximately 3 tablespoons of the yogurt mixture into each muffin cavity over the granola layer.
Use the back of a spoon to gently spread the filling into an even layer. Lightly tap the muffin pan on the countertop a few times to help the mixture settle.
Place the pan in the freezer for about 30 minutes so the filling can firm up slightly.
While the cups are chilling, combine the chocolate chips and coconut oil in a microwave-safe bowl. Microwave in 30-second intervals, stirring after each interval. Once nearly melted, continue heating in 10-second intervals until smooth.
Remove the muffin pan from the freezer and spoon or drizzle the melted chocolate evenly over each yogurt cup.
If desired, sprinkle flaky sea salt or extra granola over the chocolate before it hardens.
Return the pan to the freezer and freeze for at least 45 minutes or overnight until the Frozen Yogurt Peanut Butter Cups are completely firm.
Before serving, let the cups rest at room temperature for 20 to 30 minutes so they soften slightly and develop their best creamy texture.