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+ servings
A cupcake with crumble on top of the frosting.

Apple Crisp Cupcakes

These apple crisp cupcakes are made up of a fluffy vanilla cupcake, apple pie filling, a caramel cream cheese frosting, and a buttery, cinnamon crumble on top. Every bite screams autumn!
Course Dessert
Cuisine North American
Prep Time 30 minutes
Cook Time 55 minutes
Total Time 1 hour 25 minutes
Servings 12 cupcakes
Calories 554kcal
Author Nina


  • one 12 cup muffin tin


Vanilla Cupcakes

  • 1 ⅔ cup all purpose flour
  • ½ teaspoon baking powder
  • ¼ teaspoon baking soda
  • ½ teaspoon salt
  • ½ cup unsalted butter
  • 1 cup granulated sugar
  • 2 large eggs
  • ¼ cup vanilla yogurt room temperature
  • 2 teaspoons vanilla extract
  • cup whole milk room temperature

Apple Pie Filling

  • 2 cups apples peeled and chopped
  • ½ cup water
  • ¼ cup brown sugar packed
  • ½ teaspoon ground cinnamon
  • teaspoon ground nutmeg
  • 1 tablespoon cornstarch

Crumble Topping

  • 2 tablespoons all purpose flour
  • 1 tablespoon granulated sugar
  • 1 tablespoon brown sugar packed
  • teaspoon ground cinnamon
  • 2 tablespoons salted butter cold, diced

Caramel Cream Cheese Frosting

  • 8 oz cream cheese room temperature
  • ¼ cup salted butter room temperature
  • 3 tablespoons caramel sauce
  • 1 teaspoon vanilla extract
  • 4 cups powdered sugar


  • Vanilla Cupcakes
  • Preheat oven to 350°F and line a muffin tin with cupcake liners.
  • In a medium bowl, whisk flour, baking powder, baking soda, and salt together.
  • In a large bowl, beat butter and sugar together until creamy, about 4 minutes.
  • Add in eggs, one at a time, and mix until each one is combined. Mix in vanilla yogurt and vanilla extract.
  • Add half the dry ingredients and mix until just combined. Pour in milk and mix, and then add the rest of the dry ingredients. Mix until just combined.
  • Fill cupcake liners with the batter until ⅔ds full. Bake for 15-18 minutes, or until a toothpick inserted in the center comes out clean.
  • Allow cupcakes to cool completely before assembly.
  • Apple Pie Filling
  • Place apples, water, brown sugar, cinnamon, and nutmeg in a small saucepan. Stir to combine. Add cornstarch and stir to combine.
  • Heat over medium heat until the filling thickens and the apples soften. Remove from heat and use a potato masher to mash the apple chunks to the size of a pea.
  • Cool the apple pie filling in the refrigerator until ready to assemble cupcakes.
  • Crumble Topping
  • Preheat oven to 350°F and line a baking sheet with parchment paper.
  • In a small bowl, whisk flour, sugars, and cinnamon together. Use a fork or pastry cutter to incorporate the butter into the dry ingredients. The butter should be pea sized and well incorporated when done.
  • Spread the crumbs on the baking sheet and bake for 10-15 minutes. Stir frequently so the crumbs do not bake into a whole piece.
  • Bake until the crumbs are golden. Remove from oven to a wire rack and stir again. Let it cool down before using.
  • Store cooled crumble in an airtight container at room temperature.
  • Caramel cream cheese frosting
  • Beat cream cheese and butter together until smooth. Add caramel sauce and vanilla extract and beat until combined.
  • Add in icing sugar and beat until combined.
  • Assembly
  • Core cupcakes with a knife or a cupcake corer.
  • Carefully spoon apple pie filling into cupcake center. Gently pat it in to get as much filling as possible in.
  • Use a medium round piping tip to pipe frosting onto cupcakes.
  • Sprinkle crumble on top of the cupcakes.
  • Store cupcakes airtight in the refrigerator for up to 5 days.


  1. The vanilla cupcake, apple pie filling, and the crumble can all be made a day ahead to make assembly easier. The cupcakes and crumble should be stored at room temperature, and the apple filling filling in the fridge.
  2. I suggest using a combination of tart and sweet apples such as Granny Smith and Macintosh. Use whichever apples you prefer though. Even just one type is fine.
  3. Make sure you stir the crumble frequently as it bakes. It will bake in one giant glob if not.
  4. Leftover cupcakes should be stored in the refrigerator for up to 5 days.


Serving: 12g | Calories: 554kcal | Carbohydrates: 87g | Protein: 5g | Fat: 22g | Saturated Fat: 13g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 6g | Trans Fat: 1g | Cholesterol: 84mg | Sodium: 284mg | Potassium: 128mg | Fiber: 1g | Sugar: 70g | Vitamin A: 752IU | Vitamin C: 1mg | Calcium: 75mg | Iron: 1mg