Best Apple Pie Cupcakes Recipe for Thanksgiving

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Cozy, comforting, and fruity, apple pie cupcakes capture all the flavors of a classic apple pie in handheld form.

Soft cake is filled or topped with spiced apples and finished with a light cinnamon frosting, giving each bite that nostalgic, homemade feel.

Enjoy a batch of apple pie cupcakes and savor the warm, spiced flavors that make apple pie everyone’s favorite.

How to Make Apple Pie Cupcakes

Apple pie cupcakes are simple to make and perfect for dessert, brunch, or an anytime treat.

A sprinkle of cinnamon sugar or a small crumble topping takes them from great to unforgettable.

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How to Get Your Apple Pie Cupcakes Just Right

Mastering Apple Pie Cupcakes is all about balance.

Soft, cinnamon-scented sponge, gooey apple filling, and a light mascarpone frosting.

Follow these expert tips to make sure every batch turns out bakery-perfect:

1. Serve at the Right Temperature

Mascarpone frosting tastes best when slightly chilled, but the cupcakes themselves should be room temperature.

Let refrigerated cupcakes sit out for 15–20 minutes before serving to bring back their soft, fluffy texture.

2. Start with Room Temperature Ingredients

Butter, eggs, and milk should all be at room temperature before mixing.

This helps the batter blend smoothly, giving you cupcakes with a fine, even crumb instead of dense or unevenly baked centers.

3. Don’t Overmix the Batter

Once you add the flour, mix only until there are no visible streaks.

Overmixing develops gluten, which makes cupcakes tough instead of soft and tender.

4. Use Fresh Apples for the Filling

Choose firm, slightly tart apples like Granny Smith or Pink Lady for the best texture and flavor balance.

Dice them small so they soften evenly while cooking — mushy or overly chunky apples can ruin the cupcake’s texture.

5. Let the Filling Cool Completely

Never fill or frost warm cupcakes.

Adding apple filling while it’s still warm will make the centers soggy and cause the frosting to melt.

Prepare the filling ahead of time and allow it to cool to room temperature before assembling.

6. Watch Your Bake Time

Cupcakes bake quickly — start checking at the 20-minute mark. A clean toothpick test means they’re ready.

Overbaking dries out the crumb, while underbaking can leave the centers sunken and sticky.

7. Chill Your Frosting Tools

Mascarpone frosting whips best when everything is cold — bowl, beaters, and cream.

Overbeating or using warm ingredients can cause it to curdle or lose structure. Stop as soon as it’s thick and pipeable.

8. Assemble Right Before Serving

For the freshest taste and best texture, fill and frost your cupcakes just before serving.

If you’re prepping ahead, store the cupcakes, filling, and frosting separately in the fridge and assemble a few hours before guests arrive.

9. Avoid Overfilling

Add about one tablespoon of apple filling per cupcake.

Too much will make the centers burst or leak when you pipe the frosting.

10. Enhance the Flavor

A light drizzle of the reserved apple syrup or a sprinkle of cinnamon sugar on top makes the cupcakes extra aromatic and visually stunning.

Apple Pie Cupcakes

Recipe by Kelly
Servings

12

cupcakes
Prep time

30

minutes
Cooking time

25

minutes

This full apple pie cupcakes recipe captures all the cozy flavors of classic apple pie in a perfectly sized cupcake.

Ingredients

  • For the Cupcakes
  • 113g (½ cup) unsalted butter, room temperature

  • 100g (½ cup) granulated sugar

  • 50g (¼ cup) brown sugar

  • 2 eggs, room temperature

  • ½ teaspoon vanilla extract

  • 120g (½ cup) whole milk, room temperature

  • 185g (1½ cups) all-purpose flour

  • 1 teaspoon ground cinnamon

  • ½ teaspoon salt

  • ½ teaspoon baking powder

  • ½ teaspoon baking soda

  • ½ teaspoon white vinegar

  • Apple Pie Filling:

  • 330g (2½ cups) apples, peeled and diced

  • ½ teaspoon freshly squeezed lemon juice

  • 50g (¼ cup) brown sugar

  • 30g (2 tablespoons) unsalted butter

  • 1 teaspoon ground cinnamon

  • Mascarpone Frosting
  • 150g (⅔ cup) cold mascarpone cheese (high-fat recommended)

  • 120g (½ cup) heavy cream (36% fat), very cold

  • 40g (⅓ cup) powdered sugar, sifted

  • ½ teaspoon vanilla extract

Directions

  • For the Cupcakes
  • Heat your oven to 175°C / 350°F (no fan). Line a 12-cup muffin pan with paper liners and set aside.
  • In a large mixing bowl, beat the softened butter, granulated sugar, and brown sugar together for about 2–3 minutes until the mixture is pale and fluffy.
  • Mix in the eggs, one at a time, scraping down the sides of the bowl as needed. Stir in the vanilla extract until fully incorporated.
  • In a separate bowl, sift together the flour, ground cinnamon, baking powder, and salt.
  • With your mixer on low speed, add the dry ingredients to the butter mixture in three additions, alternating with the milk. Begin and end with the dry ingredients. Mix just until combined—overmixing can make the cupcakes dense.
  • In a small cup, combine the baking soda and white vinegar. It will foam up quickly—immediately fold this mixture into your batter until evenly distributed.
  • Divide the batter evenly between the cupcake liners, filling each about ¾ full. Bake for 20–22 minutes, or until a toothpick inserted in the center comes out clean.
  • Let the cupcakes cool in the pan for 5 minutes, then transfer them to a wire rack to cool completely before adding the filling or frosting.
  • For the Apple Pie Filling
  • Dice the peeled apples into small chunks and toss them with lemon juice to prevent browning.
  • Add the apples, brown sugar, butter, and cinnamon to a medium saucepan. Cook over medium heat for 5–10 minutes, stirring occasionally, until the apples are tender and coated in a thick syrup.
  • Let the mixture cool to room temperature before using. Save a bit of the thickened “apple caramel” sauce to drizzle over the cupcakes later.
  • For the Mascarpone Frosting
  • In a chilled mixing bowl, combine the cold mascarpone cheese, cold heavy cream, powdered sugar, and vanilla extract.
  • Using an electric hand mixer, beat on medium speed for 2–3 minutes until the frosting becomes thick and pipeable. Stop mixing as soon as it holds stiff peaks—overbeating will cause it to separate.
  • For the Decoration
  • Once the cupcakes have fully cooled, use a small knife or cupcake corer to cut a shallow hole in the center of each. Fill each cupcake with about 1 tablespoon of apple pie filling.
  • Fit a piping bag with a Wilton 1M tip (or your favorite nozzle) and swirl the mascarpone frosting over the top of each cupcake.
  • Spoon a bit of the reserved apple filling—or the syrup—into the center of the frosting for a delicious finishing touch.
  • Optional Decoration
  • If you have leftover pie dough, cut small leaf shapes using a knife or leaf-shaped cutter, bake until golden, and use them to decorate the cupcakes.
  • Enjoy the cupcakes fresh! Any leftovers should be stored in an airtight container in the refrigerator for 1–2 days. Bring to room temperature before serving for the best flavor and texture.

Variation Tips

These Apple Pie Cupcakes are delicious as they are, but a few clever tweaks can make them even more exciting or suited to different preferences.

Whether you want to play with the flavors, textures, or dietary options.

Here are some simple yet creative ways to switch things up:

1. Try Different Apple Varieties

Change up the flavor profile by using a mix of apple types. Tart Granny Smiths add brightness, Honeycrisp brings natural sweetness, and Pink Lady gives a balanced fruity aroma.

Mixing two kinds makes the filling more complex and flavorful.

2. Add a Caramel Twist

Drizzle homemade or store-bought salted caramel sauce inside the cupcake cavity before adding the apple filling or over the frosting for a caramel-apple pie flavor.

It pairs beautifully with the mascarpone frosting.

3. Swap the Frosting

If you prefer something richer, use cream cheese frosting instead of mascarpone.

For a lighter option, top with cinnamon whipped cream or a swirl of brown sugar buttercream.

4. Make It Crunchy

Add a bit of texture by sprinkling crushed Biscoff biscuits, graham cracker crumbs, or toasted pecans on top of the frosting.

You can also press a small pie crust “leaf” or crumble on top for that rustic pie-like finish.

5. Infuse More Spice

For a warmer, bakery-style flavor, blend in a pinch of nutmeg, allspice, or cardamom with the cinnamon in the cupcake batter or the apple filling. This creates a cozy fall twist.

6. Dairy-Free Option

Swap butter with a plant-based alternative, use almond or oat milk instead of whole milk, and substitute the mascarpone with a dairy-free cream cheese or coconut-based whipped topping.

7. Gluten-Free Adaptation

Use a 1:1 gluten-free all-purpose flour blend that already contains xanthan gum.

The texture will remain soft and tender if you avoid overmixing.

8. Add a Boozy Note (Adults Only)

For a grown-up version, add a splash (1–2 teaspoons) of spiced rum or bourbon to the apple filling. It enhances the warmth of the spices without overpowering the dessert.

9. Transform Into a Layered Dessert

Turn the recipe into mini trifle cups.

Layer chunks of cupcake with apple filling and mascarpone frosting in glass jars for a no-fuss, spoonable treat perfect for parties.

10. Go Festive

In winter, sprinkle the frosted cupcakes with edible gold dust, cinnamon sugar, or tiny pastry stars for a holiday-worthy presentation that feels like a mini apple pie on every plate.

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Storage Tips

To keep your Apple Pie Cupcakes as soft, flavorful, and fresh as the day they were made, proper storage is key, especially since the recipe contains a moist apple filling and mascarpone frosting.

Here’s how to store them correctly and enjoy every bite even days later:

1. At Room Temperature (Short-Term Storage)

  • Best for: Unfrosted cupcakes only.
  • Store the plain cupcakes (without filling or frosting) in an airtight container at room temperature for up to 2 days.
  • Keep them away from direct sunlight or heat to prevent the butter from melting or the cupcakes from drying out.
  • Once filled and frosted, they should be refrigerated due to the mascarpone.

2. In the Refrigerator (Best for Frosted Cupcakes)

  • Best for: Assembled cupcakes with apple filling and mascarpone frosting.
  • Store cupcakes in an airtight container with enough space so the frosting doesn’t get squished. You can place parchment paper between layers if stacking is necessary.
  • Refrigerate for up to 3 days. Before serving, let them sit at room temperature for 20–30 minutes so the frosting softens and the flavors bloom again.
  • Avoid leaving them uncovered in the fridge — it can dry out both the cupcake and frosting.

3. Freezing (For Longer Storage)

  • Best for: Unfrosted or filled cupcakes. Avoid freezing mascarpone frosting as it may separate once thawed.
  • Freeze cooled, unfilled cupcakes in an airtight, freezer-safe container or wrap each cupcake tightly in plastic wrap and then in foil.
  • They’ll stay fresh for up to 2 months.
  • To use, thaw at room temperature for about 1 hour, then fill and frost as desired.
  • If freezing filled cupcakes, allow them to thaw slowly in the fridge overnight to prevent the apple filling from getting too watery.

4. Reheating or Refreshing Tips

  • For that freshly baked feel, you can warm the unfrosted cupcakes in the microwave for 10–15 seconds or in a preheated oven at 300°F (150°C) for about 5 minutes.
  • Never reheat frosted cupcakes, as the mascarpone frosting will melt.

Storage Mistakes to Avoid

  • Don’t leave frosted cupcakes out overnight as mascarpone is dairy-based and spoils easily.
  • Avoid the freezer for frosted cupcakes. The frosting texture will break once thawed.
  • Don’t store warm cupcakes. Always let them cool completely before sealing to prevent condensation and sogginess.

Pro Tip: For the best presentation, add the final spoonful of apple pie filling and decorative touches just before serving. It keeps the topping fresh, glossy, and bakery-perfect.

Save for Later to Your Pinterest Board

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FAQs

Can I use a different type of apple for the filling?

Yes! Firm, slightly tart apples like Granny Smith, Honeycrisp, or Braeburn work best because they hold their shape and balance the sweetness of the cupcake. Softer varieties like Golden Delicious can be used but may turn mushy, so cook them for slightly less time.

Can I make these cupcakes dairy-free or vegan?

You can swap butter for plant-based margarine and use a non-dairy milk like almond or oat milk. For mascarpone frosting, you can try vegan cream cheese or coconut cream, but note the texture and flavor will be slightly different from the original.

How do I prevent the cupcakes from sinking in the middle?

Avoid overmixing the batter once you add the flour; overmixing develops gluten and can make cupcakes dense or cause sinking.
Ensure eggs and butter are at room temperature to create a smooth, aerated batter.
Bake immediately after mixing, and don’t open the oven door during the first 15–18 minutes of baking.

How long will these cupcakes stay fresh?

Unfrosted cupcakes: 2 days at room temperature.
Filled and frosted cupcakes: 3 days in the refrigerator.
Unfrosted cupcakes (frozen): Up to 2 months in a freezer-safe container. Always thaw before adding frosting or filling.

Can I prepare these cupcakes in advance?

Absolutely! You can:
Bake the cupcakes a day or two ahead and store them unfrosted.
Make the apple filling ahead of time and refrigerate it.
Frost and fill the cupcakes just before serving for the freshest taste and best presentation.

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