Prepare the Cupcake Pan: Preheat the oven to 350°F and line a 16-cup cupcake tin with paper liners, or grease the cups with butter and flour.
Sift the Dry Ingredients: Sift the all-purpose flour, baking powder, baking soda, and fine sea salt together into a bowl, then set aside.
Cream the Butter: Place the softened butter in the bowl of an electric mixer and beat at medium speed for about 1 minute.
Add the Sugar: Add the granulated sugar and continue creaming for about 2 minutes, until the mixture is creamy and fluffy, scraping down the sides of the bowl as needed.
Incorporate the Eggs: Add the eggs one at a time, mixing until each egg is combined before adding the next.
Add the Vanilla: Mix in the vanilla extract until incorporated.
Add the Milk: Slowly add the room-temperature milk, stirring until combined.
Combine the Batter: Add the sifted dry ingredients and fold until just incorporated.
Fill the Cupcake Tin: Divide the batter evenly among the prepared cupcake cups, filling each about two-thirds full.
Bake the Cupcakes: Bake at 350°F for about 15 minutes, rotating the pan during baking so the cupcakes cook evenly.
Check for Doneness: If necessary, bake for a couple of additional minutes. The cupcakes are ready when the tops gently spring back after being pressed.
Cool the Cupcakes: Allow the cupcakes to cool completely before filling and frosting.
Cook the Apples: Place the chopped apples, lemon juice, 2 tablespoons of water, and the optional cinnamon stick in a small saucepan. Cook over medium heat until the apples are softened but still hold their shape rather than falling apart.
Adjust for the Apples: Allow more or less cooking time as needed because softer varieties of apples cook faster.
Remove the Cinnamon Stick: Take the cinnamon stick out of the saucepan once the apples have softened.
Season the Filling: Add the brown sugar, ground cinnamon, ground nutmeg, and kosher salt. Cook for 1 minute to dissolve the brown sugar.
Make the Slurry: In a small container, combine 1 tablespoon cornstarch with 2 tablespoons water and mix until smooth.
Thicken the Filling: Stir the cornstarch mixture into the apples and cook for 1–2 minutes, until the apple filling has thickened.
Chill the Filling: Transfer the apple filling to a bowl and refrigerate until completely cooled before using.
Prepare the Crumble: Preheat the oven to 350°F. Combine the all-purpose flour, white sugar, brown sugar, and cinnamon in a bowl.
Add the Butter: Add the cold diced butter to the dry mixture.
Form the Crumbs: Work the butter into the dry ingredients using a fork or your hands until the mixture resembles coarse meal and no visible pieces of butter remain.
Bake the Crumble: Spread the crumb mixture over a baking sheet lined with parchment paper or a silicone baking mat. Bake at 350°F for 10–15 minutes, stirring frequently during baking to break up the crumbs.
Finish the Crumble: Stir the crumbs again immediately after removing them from the oven. Continue baking until the crumbs are golden, then let them cool completely.
Store the Crumble: Once cooled, keep the crumble in an airtight container at room temperature for up to 5 days.
Sift the Frosting Ingredients: Sift the powdered sugar together with the ground Ceylon cinnamon and set aside.
Cream the Frosting Base: Beat the softened cream cheese and butter in an electric mixer for about 2 minutes, until light and fluffy.
Add the Vanilla: Mix in the vanilla extract until combined.
Add the Powdered Sugar: Turn the mixer off and add the powdered sugar and cinnamon mixture to the bowl.
Incorporate the Sugar: Turn the mixer to low and mix until the powdered sugar is incorporated and no streaks of dry sugar remain.
Whip the Frosting: Increase the mixer to medium-high and beat the frosting for 1 minute.
Store the Frosting: If preparing it ahead, keep the frosting covered in the refrigerator for up to 5 days. Cover the bowl with a lid or plastic wrap to prevent the surface from drying and becoming hard.
Core the Cupcakes: Use a spoon to remove the center of each cooled cupcake, creating a space for the apple filling.
Fill the Centers: Spoon some chilled apple pie filling into each cupcake.
Frost the Cupcakes: Frost around the filled center, leaving a small opening in the middle.
Add More Apple Filling: Spoon a little more apple pie filling into the opening in the center of the frosting.
Add the Crumble: Finish each cupcake with some of the cooled crumble topping.
Store the Cupcakes: Keep the assembled cupcakes refrigerated for up to 5 days.
