Place butter and maple syrup in a large bowl and place into the microwave. Heat in 30 second intervals, stirring after every 30 seconds, until butter is melted, about 1 to 1 1/2 minutes. Remove bowl from microwave and add in vanilla, cinnamon, salt, and nutmeg. Stir until thoroughly combined. Add in oats, almonds, coconut, and flax meal. Stir until mixture is thoroughly combined.

Generously grease a standard muffin tin with nonstick baking spray with flour.

Divide oat mixture evenly between the muffin cups, about 2 heaped tablespoons per cup. With wet hands, press mixture into the bottom and up the sides of each cup. Place the pan into the fridge to chill for 15 minutes.

Preheat the oven to 350 degrees F (175 degrees C).

Bake chilled granola cups in the preheated oven until the outside edges of cups turn golden brown,  25 to 30 minutes. Remove cups from the oven; cool to room temperature in the pan, about 30 minutes.

Use an offset spatula or butter knife to pop them out of the pan. To serve, fill each granola cup with yogurt and top with berries. Serve immediately.