Preheat your oven to 350°F (175°C) and lightly grease a small oven-safe baking dish or large ramekin with a small amount of ghee.
In a medium mixing bowl, whisk together the Greek yogurt, eggs, vanilla extract, and sea salt until the mixture is completely smooth and creamy.
Pour the yogurt custard base into the prepared baking dish, smoothing the surface with a spoon.
Core and thinly slice the apple, then arrange the slices in an overlapping pattern across the top of the yogurt mixture.
In a separate small bowl, melt the remaining ghee and stir in the chopped pecans, rolled oats, maple syrup, and ground cinnamon until the mixture is well combined and crumbly.
Sprinkle the pecan crumble topping evenly over the apple slices.
Bake for 30 to 35 minutes, or until the custard is set and the pecan topping is golden brown and fragrant.
Remove from the oven and allow the dish to cool for at least 5 minutes to let the custard firm up before serving.