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Apple Crisp Cheesecake Muffins – With Cinnamon Apples and Crumb Topping

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These Apple Crisp Cheesecake Muffins combine soft, cinnamon-spiced muffins with diced apples, creamy cheesecake filling, and a buttery oat crisp topping. Finished with a simple vanilla glaze, they’re a cozy fall treat for breakfast, dessert, or an afternoon snack.

  • Total Time: 50 minutes
  • Yield: 16–18 muffins

Ingredients

Scale

Crisp Topping:

  • 1/2 cup all-purpose flour
  • 1/3 cup quick-cooking oats
  • 1/3 cup light brown sugar
  • 3/4 teaspoon ground cinnamon
  • 1/4 teaspoon ground nutmeg
  • 1/4 cup unsalted butter, melted

Cinnamon-Sugar:

  • 2 tablespoons light brown sugar
  • 1/2 teaspoon ground cinnamon

Apple Filling:

  • 2 medium apples, such as Granny Smith or Gala, peeled and diced into 1/3-inch pieces
  • 2 tablespoons granulated sugar
  • 1 teaspoon ground cinnamon

Muffins:

  • 1 1/2 cups all-purpose flour
  • 1 1/2 teaspoons baking powder
  • 1/2 teaspoon salt
  • 1/2 cup unsalted butter, at room temperature
  • 2/3 cup granulated sugar
  • 2 eggs, at room temperature
  • 1 1/2 teaspoons vanilla extract
  • 1/2 cup milk, at room temperature

Cheesecake Filling:

  • 12 oz brick-style cream cheese, at room temperature
  • 1/2 cup granulated sugar
  • 3 tablespoons all-purpose flour
  • 1 teaspoon vanilla extract
  • 1 egg

Vanilla Icing:

  • 3/4 cup powdered sugar
  • 2 tablespoons milk or cream
  • 1/2 teaspoon vanilla extract

Instructions

Make the crisp topping:

  1. Preheat the oven to 350°F and line a standard muffin pan with paper liners. This recipe makes approximately 16–18 muffins.
  2. In a bowl, combine the flour, quick-cooking oats, light brown sugar, cinnamon, and nutmeg. Add the melted butter and mix with a fork until evenly moistened. Set aside.

Prepare the cinnamon sugar and apples:

  1. In a small bowl, mix 2 tablespoons light brown sugar with 1/2 teaspoon cinnamon. Set aside for layering.
  2. Peel and dice the apples into small 1/3-inch pieces. Toss with 2 tablespoons granulated sugar and 1 teaspoon cinnamon. Set aside.

Make the muffin batter:

  1. Beat the room-temperature butter, sugar, and vanilla extract together.
  2. Add the eggs and mix until combined.
  3. Incorporate the flour, baking powder, and salt, mixing until combined.
  4. Slowly pour in the milk and mix just until combined. Scrape down the bowl with a rubber spatula to ensure there are no lumps. Avoid overmixing.

Make the cheesecake filling:

  1. Mix the softened cream cheese with the sugar, flour, and vanilla extract until combined.
  2. Add the egg and mix just until incorporated. Set aside.

Assemble and bake:

  1. Place about 1 heaping tablespoon of muffin batter into the bottom of each paper liner.
  2. Scatter diced apples over the batter, gently pressing them in. Sprinkle generously with the cinnamon-sugar mixture.
  3. Spoon a heaping tablespoon of cheesecake filling over the apples and gently spread it with the back of the spoon.
  4. Add more apple pieces on top and sprinkle with cinnamon sugar again.
  5. Spread more muffin batter over the top until each liner is about three-quarters full.
  6. Sprinkle the crisp topping evenly over the muffins.
  7. Bake for 23–28 minutes, or until a toothpick inserted into the center comes out clean.
  8. Cool in the pan for 5 minutes, then transfer the muffins to a wire rack to cool completely.

Make the vanilla icing:

  1. Stir together the powdered sugar, milk or cream, and vanilla extract until smooth.
  2. Drizzle the icing over the cooled muffins before serving.

Notes

  • Yield: Approximately 16–18 muffins.
  • Apples: Granny Smith or Gala apples are suggested. Peel and dice them into small 1/3-inch pieces.
  • Room-temperature ingredients: Use room-temperature butter, eggs, milk, and cream cheese as specified for easier mixing.
  • Do not overmix: Mix the muffin batter only until the ingredients are combined.
  • Cooling: Let the muffins rest in the pan for 5 minutes before transferring them to a wire rack. Cool completely before adding the vanilla icing.
  • Baking time: Bake for 23–28 minutes, checking for doneness with a toothpick.
  • Author: Emma
  • Prep Time: 25 minutes
  • Cook Time: 25 minutes
  • Category: Dessert, Breakfast
  • Method: Baking
  • Cuisine: American