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Preheat the oven to 350 and line two 12-cup muffin tins with cupcake liners.
Toss the apple chunks with 2 tablespoons of flour (2 tablespoons plus two cups) to keep the apples from sinking to the bottom of each cupcake well.
Whisk the 2 cups flour, baking powder, baking soda, salt, cinnamon (1/2 teaspoon), and nutmeg together in a medium bowl.
In the bowl of a stand mixer fitted with the paddle attachment, cream the butter (8 tablespoons) and sugar (1 cup) together on medium speed for 3 minutes until light and fluffy. Add the eggs one at a time, stirring on low speed until combined. Stir in the vanilla extract.
Add the dry ingredients in three batches, alternating with the addition of the buttermilk in two batches, mixing on low speed until all ingredients are just incorporated.
Stir the apple chunks into the batter with a spatula.
Make the streusel topping by whisking the flour (1/2 cup), brown sugar (1/2 cup) and cinnamon (1 teaspoon) together in a medium mixing bowl. Add the butter (4 tablespoons, at room temperature, cut into 1/2-inch cubes) to the dry ingredients by working it in with your fingers or a pastry blender until moist clumps form.
Scoop the batter into the prepared muffin tins, and top each cupcake well with a generous handful of streusel topping.
Bake for 20-25 minutes or until the streusel topping is crisp and brown.
Remove from the muffin tins and cool on wire racks.