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Apple pie cupcakes capture all the comforting flavors of fall in a delicious shareable mini cake. Soft, tender spice cupcakes infused with cinnamon, nutmeg, and cloves, while a hidden apple filling surprises you with each bite. Topped with a creamy maple vanilla buttercream, these cupcakes feel indulgent without being fussy.

From the light, airy crumb to the warm, spiced filling and the rich buttercream frosting, every element plays a part in enjoying the taste of fall baking season.

Close up of vanilla frosted cupcakes filled with apple pie filling.

Key Ingredients & Test Notes

  • All Purpose Flour at a lower protein of 10% protein level gives these cupcakes their tender crumb.
    • Test Note: Sift the flour for an extra airy batter and a more uniform cupcake dome. Cake flour made with a softer wheat and a protein level of 8-9% can be substituted for a more delicate crumb.
  • Dark Brown Sugar sweetens with a slight hint of molasses that contributes to a tender crumb that keeps the cupcakes moist.
    Cinnamon, Nutmeg, and Cloves are warming fall spices that bring a subtle hint of depth without overwhelming.
    • Test Note: Toasting these spices briefly in a dry pan before adding them can really intensify their flavor.
  • Unsalted Butter that is softened, not melted, is needed to trap air when whipped with sugar for a fluffy baked cupcake crumb texture.
  • Sunflower Oil replaces some of the fat for a moist tender cupcake.
  • Eggs give structure and lift while keeping the cupcake light and airy. They’re whipped into the butter and sugar to create a fluffy base.
  • Crème Fraîche and Whole Milk combine for a richer cake that stays moist longer.
  • Granny Smith Apples are perfectly tart baking apples that balance the sweetness of the cupcake and buttercream beautifully. Their firmness ensures that the filling has a nice bite even after cooking.
    • Test Note: Slightly macerate them with sugar and cinnamon before cooking to enhance their natural flavor. Toss the chopped apples with the spices and let sit for 30 minutes.
Single cupcake with wrapped folded down, topped with vanilla buttercream and apple pie filling.

Helpful Tips

  • Cool Completely Before Filling: Let the cupcakes cool fully before coring or frosting. Warm cupcakes can make the buttercream melt or the apple filling run.
  • Coring for Apple Filling: Use a small melon baller or a ¾–1 inch cookie cutter to remove a bit of the center from each cupcake. Fill with apple pie filling so it’s level with the remaining top for a perfectly even frosting surface.
  • Smooth Buttercream: For a silky maple vanilla buttercream, whip the butter first, then add maple syrup and cream gradually before adding powdered sugar. This prevents a gritty or stiff texture.
  • Frost Like a Pro: Use a #4B star tip for a tight swirl. Twist the top of the piping bag to prevent leaks, and keep consistent pressure as you pipe from the edge spiraling inward. Finish by pressing down gently and pulling up to create a classic peak.
  • Maple Cinnamon Sprinkle: For a final touch, stir together 1 tablespoon cinnamon with 2 tablespoons sparkling sugar and sprinkle lightly over the frosting. I love how it adds a sparkly color contrast.
Unfrosted brown sugar cupcakes on a wooden cutting board.

How to Make Apple Pie Cupcakes

Start by preheating your oven to 350°F (180°C) and lining your cupcake pans with 12 paper liners. Whisk together your dry ingredients, flour, rising agents, and those cozy spices. Set that aside. In a large bowl cream together the softened butter, oil and sugars until light and fluffy. Mix in one egg a time, then mix in the crème fraîche and vanilla. Finally, mix in the half the flour, alternating with the milk and repeat.

Use a medium ice cream scoop (about 3 tablespoons) to portion the batter into each cupcake liner, filling them about ¾ of the way up. Pop them in the oven for 16–18 minutes, or until a toothpick inserted in the center comes out clean. Let them cool for a few minutes in the pan, then transfer cupcakes to a wire rack to cool completely.

Make your apple pie filling. In a small saucepan over medium heat, cook your chopped apples with butter, sugar, and a pinch of cinnamon and nutmeg. Once they soften, whisk in the cornstarch slurry to thicken. Let cool completely.

Once baked cupcakes are at room temp, it’s time to core and fill them. Use a melon baller or a small cookie cutter to remove the center of each cupcake, then fill with the apple pie mixture so the tops are level. Whip up your maple vanilla buttercream until silky, fill your piping bag, and swirl it over each cupcake with your favorite star piping tip.

Cupcake with a center of apple pie filling topped with vanilla frosting bitten in half.

Leftovers & Storage

Room Temperature: Store cupcakes in an airtight container at room temperature for 3–5 days. The flavors actually meld beautifully after a day, making them even more delicious.

★★★★★ Please leave a star rating and review below if you make this recipe! THANK YOU!!

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Apple Pie Cupcakes

Prep: 30 minutes
Cook: 18 minutes
Total: 48 minutes
Servings: 14 cupcakes
Brown sugar apple pie cupcakes, topped with maple vanilla buttercream frosting and filled with with homemade apple pie filling.
Click for Ingredient Details

Equipment

Ingredients

Cupcake Batter

  • 189 grams (1 ½ cups) all purpose flour, 10-11% protein, *or cake flour
  • 1 teaspoon baking powder
  • ½ teaspoon baking soda
  • ½ teaspoon fine sea salt
  • 1.5 teaspoons ground cinnamon
  • ½ teaspoon ground ginger
  • ½ teaspoon ground nutmeg
  • 220 grams (1 cup) dark brown sugar
  • 57 grams (¼ cup) unsalted butter, European style 82% butterfat, softened
  • 60 grams (¼ cup) sunflower oil
  • 2 teaspoons pure vanilla extract or vanilla bean paste
  • 100 grams (2 large) eggs
  • 80 grams ( cup) crème fraîche, *swap for sour cream
  • 60 grams (¼ cup) whole milk, room temperature

Apple Pie Filling

  • 3 large granny smith apples , cored, peeled, and chopped into 1/2-inch pieces
  • 3 tablespoons fresh lemon juice
  • 28 grams (2 tablespoons) unsalted butter
  • 1 ½ teaspoons ground cinnamon
  • ¼ teaspoon ground nutmeg
  • 73 grams ( cup) dark brown sugar
  • 10 grams (2 teaspoons) cornstarch
  • 1 tablespoon water

Maple Vanilla Buttercream

Instructions 

  • Preheat Oven to 350℉ (180℃) and line a 12-cavity cupcake pan with paper liners.
  • Whisk together the flour, baking powder, baking soda, salt, and spices in a medium bowl. Set aside.
    189 grams all purpose flour, 1 teaspoon baking powder, ½ teaspoon baking soda, ½ teaspoon fine sea salt, 1.5 teaspoons ground cinnamon, ½ teaspoon ground ginger, ½ teaspoon ground nutmeg
  • In a large bowl using a handheld mixer, cream the room-temperature butter and brown sugar until combined. Add the oil and mix again until fluffy. About 1-2 minutes.
    220 grams dark brown sugar, 57 grams unsalted butter, 60 grams sunflower oil
  • Continue on medium-low speed and beat in one egg at a time until fluffy, about 30 seconds each.
    100 grams eggs
  • Mix in the crème fraîche and vanilla.Scrape the bottom and sides of bowl as needed with a spatula to make sure everything is incorporated.
    80 grams crème fraîche, 60 grams whole milk
  • Mix in half the dry ingredients, alternating with the milk. Followed by the remaining dry ingredients until just combined.
  • Fill each paper liner ⅔ -¾ full with batter. I like to use a large cookie scoop to evenly distribute the batter amongst the paper liners.
  • Place pan on the middle oven rack and bake for 16-18 minutes or until a toothpick inserted into the center comes out clean and the tops are springy to the touch.
  • Place tray on a cooling rack for 5 minutes, before flipping them out and setting the cupcakes directly on the rack to cool completely.

Make Apple Pie Filling While Cupcakes are Baking

  • In a saucepan on medium heat, add apples, butter, spices, sugar and lemon juice. Stir slowly until butter is melted, sugar dissolves, and apples begin to soften. (4-5 min)
    3 large granny smith apples, 3 tablespoons fresh lemon juice, 28 grams unsalted butter, 1 ½ teaspoons ground cinnamon, ¼ teaspoon ground nutmeg, 73 grams dark brown sugar
  • Stir cornstarch and water in a cup to make a liquid slurry. Pour onto apple filling and stir until thickened.
    10 grams cornstarch, 1 tablespoon water
  • Remove pan from heat and set aside to cool.

Assemble

  • Use a 3/4 inch melon ball scoop or spoon to remove center from cupcake dome. Fill the whole with apple pie filling level with the top of the cupcake.
  • Pipe frosting onto the cupcake to cover the filling inside.
    1 batch maple buttercream frosting
Tried this recipe?Mention @twocupsflour or tag #twocupsflour!

About Jenn

Welcome to Two Cups Flour, a seasonal baking blog dedicated to delicious sweet and savory breakfast, breads, and desserts.

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5 Comments

  1. Jenn says:

    Yes 🙂

  2. Jenn says:

    Yes, add cream and salt with the maple syrup:)

  3. Jenn says:

    Hi Michelle! Yes you can substitute the nutmeg for all spice but I would only use 1/4 tsp allspice. Also, you can swap the Almond Milk for Whole Milk 🙂

  4. Jenn says:

    Hi Anthony, Tips for filling the cupcakes is in the post:)

  5. Jenn says:

    See above for step by step instructions:)