To make the brown butter, melt butter in a clear heavy bottom pot. Once the butter starts to foam, whisk continuously until brown bits start to form. Remove from heat, pour into clean bowl, skim the foam from the top and cool to room temperature (20-25 minutes).
Line 12 ct muffin pan with cupcake liners and preheat oven to 350F. Whisk together flour, baking powder, baking soda, salt and chai spice. Set aside.
In a stand mixer with paddle attachment, beat browned butter and sugar until smooth and well combined (3-4 minutes). Add eggs, beating well after each one until well combined. Add vanilla and almond extracts, beating until well combined.
In this order (dry ingredients, yogurt, dry, yogurt, dry), add dry ingredients to the wet alternating with the yogurt. Slowly beat each time until JUST combined. A few flour streaks is okay! Gently fold in the chopped apples until most pieces are combined into the batter.
Using a 2" cookie scopp with trigger release or a large spoon, fill each cupcake liner 3/4 to the top. Place muffin pan into preheated oven and bake at 350F for 22-25 minutes. Tops should be golden brown and a tooth pick inserted into the center should come out mostly clean.
Let cupcakes cool in the pan for 5 minutes. Genlty remove the cupcakes and cool completely before frosting (45 minutes).