Apple Pie Cupcakes with Cream Cheese Frosting Recipe

I absolutely love this Apple Pie Cupcakes with Cream Cheese Frosting Recipe because it brings the warm, cozy flavors of classic apple pie into a perfectly portable cupcake form. These cupcakes are ideal when you want something seasonal but also a little different from your usual dessert lineup — they’re great for family gatherings, potlucks, or just a comforting afternoon treat with a cup of tea.

When I first tried this recipe, I was blown away by how the apple filling stays juicy and tender without making the cupcakes soggy, and the cream cheese frosting adds the perfect balance of tangy sweetness. You’ll find that these cupcakes are proof that you don’t have to choose between pie or cake — you really can have both in one bite!

this Recipe

Ingredients You’ll Need

Every ingredient in this Apple Pie Cupcakes with Cream Cheese Frosting Recipe works together to create that iconic apple pie taste, but in individual cupcakes. Choosing ripe, tart apples and quality cream cheese really makes a difference here.

• Small tart apples: Granny Smith or similar tart apples bring bright flavor and firm texture that holds up well during cooking.
• Brown sugar: Adds warmth and depth to the apple filling, complementing the cinnamon perfectly.
• Cornstarch: Thickens the apple filling so it’s luscious but not runny.
• Ground cinnamon: A key warming spice that really ties the whole recipe together.
• Water: Helps cook the apples gently without diluting flavor.
• Cake flour: Creates a tender, light crumb in the cupcakes.
• Baking powder: Gives the cupcakes perfect rise and fluffiness.
• Salt: Enhances all the flavors and balances the sweetness.
• Unsalted butter: Use room temperature for easy creaming and richness.
• Granulated sugar: Sweetens the cupcake batter evenly.
• Large eggs: Provide structure and moisture.
• Vanilla extract: Adds a subtle but essential layer of warmth.
• Milk (dairy or non-dairy): Keeps the batter moist and tender.
• Cream cheese: Softened for smooth, tangy frosting that complements the sweet apple filling.
• Powdered sugar: Sweetens and thickens the frosting perfectly.

Variations

One of the things I love about this Apple Pie Cupcakes with Cream Cheese Frosting Recipe is how easy it is to make it your own. I often tweak it depending on what’s in my pantry or the season—feel free to get creative!

• Added Nuts: I sometimes throw in chopped walnuts or pecans into the apple filling for a nice crunch and a little extra texture that my family goes crazy for.
• Spice it Up: Adding a pinch of nutmeg or allspice along with cinnamon warms the cupcakes up even more—especially in fall.
• Gluten-Free: Swapping cake flour for your favorite gluten-free blend works well here; just be sure to check your baking powder is gluten-free too.
• Dairy-Free: I’ve tried non-dairy butter and cream cheese alternatives—just watch the consistency and adjust sugar to taste if needed.

How to Make Apple Pie Cupcakes with Cream Cheese Frosting Recipe

Step 1: Cook the Apple Filling to Perfection

In a small pot, combine the finely diced tart apples with brown sugar, cornstarch, cinnamon, and water. Cover and bring the mixture to a gentle boil over medium-high heat, then uncover and cook, stirring frequently, until the apples become tender and the liquid thickens into a luscious compote. If the mixture looks dry or starts to stick, just add a splash more water and let it cook off. I’ve found that patience here is key to getting that perfect, pie-like filling that isn’t too mushy or too runny. Once done, transfer it to a bowl and let it cool completely – this prevents the filling from steaming the cupcakes later.

Step 2: Prep and Mix the Cupcake Batter

Preheat your oven to 350°F (175°C) and line a 12-hole muffin pan with parchment liners. In a small bowl, stir together cake flour, baking powder, cinnamon, and salt. In a large bowl, beat the softened butter until creamy using a hand mixer, then add granulated sugar and continue beating until fluffy. Incorporate eggs one at a time, mixing well after each addition, then beat in vanilla extract. Now, alternate adding the dry ingredients and milk to the wet mix — sift half the dry ingredients in, mix lightly, add half the milk, mix again, then repeat. Be careful not to overmix; you want everything combined and smooth, but the batter should stay light and airy.

Step 3: Bake and Cool

Fill each cupcake liner about two-thirds full with batter – this helps your cupcakes rise nicely without getting too domed. Pop them into the oven and bake for about 20 minutes, or until a toothpick inserted into the center comes out clean. I usually let the cupcakes rest in the pan for 5 to 10 minutes before transferring them to a wire rack to cool completely. This little rest makes them easier to handle and stops them from getting soggy on the bottom.

Step 4: Whip Up the Cinnamon Cream Cheese Frosting

In a bowl, beat softened butter until squishy and creamy, then add softened cream cheese, powdered sugar, ground cinnamon, and vanilla extract. Keep beating on low speed until the frosting is smooth, thick, and perfectly spreadable. You want a frosting that’s rich but not overly sweet, with just a hint of cinnamon to tie in with your cupcake’s flavor.

Step 5: Assemble Your Apple Pie Cupcakes

Carefully scoop out the center of each cupcake using a small melon baller or a sharp knife, removing about half the depth. Fill the hollow with your cooled apple compote, then add a little more on top, gently pressing it down but leaving a bit of cupcake edge bare. Using a piping bag fitted with a small ribbon piping tip, pipe two crisscrossed lines of frosting over the apple topping. Switch to an open star tip and pipe a pretty border around the cupcake’s edge to finish it off. It’s these details that make the cupcakes look as gorgeous as they taste.

How to Serve Apple Pie Cupcakes with Cream Cheese Frosting Recipe

Garnishes

I like to keep garnishes simple and elegant. A light dusting of cinnamon or a small fresh apple slice on top adds a gorgeous finishing touch. Sometimes, I sprinkle a little chopped pecans around the frosting border — it not only looks incredible but adds a wonderful crunch.

Side Dishes

If you’re serving these cupcakes at a brunch or party, pairing them with warm spiced cider or a creamy chai latte makes the flavors pop. They also team wonderfully with a scoop of vanilla ice cream for dessert or alongside a cheese and charcuterie board for a unique twist.

Creative Ways to Present

I’ve found that presenting these cupcakes on a rustic wooden board with autumn leaves, cinnamon sticks, and mini gourds sets a cozy seasonal vibe. For birthdays or celebrations, piping fun apple shapes or leaves with colored frosting brings an extra playful touch. Wrapping each cupcake in a clear cellophane bag tied with twine is perfect for gifting or party favors.

Make Ahead and Storage

Storing Leftovers

I keep leftover cupcakes stored in an airtight container in the refrigerator to keep the cream cheese frosting fresh and firm. They stay great for up to 3 days this way, and I’ve found that letting them come to room temperature before serving restores some of that fresh-baked softness.

Freezing

Freezing these cupcakes is a bit tricky because of the cream cheese frosting, but it’s doable if you freeze them unfrosted. I usually scoop and fill the apples ahead, freeze the cupcakes, and defrost fully before adding frosting. This way, you avoid sogginess or frosting melting issues.

Reheating

If you want to enjoy a leftover cupcake warm, remove it from the fridge and let it sit out for 10 minutes, then pop it in the microwave for 10-15 seconds (without frosting) if you prefer a slightly warmed bite. Avoid reheating the frosted cupcake directly—cream cheese can get oily or separate.

FAQs

Final Thoughts

If you’re looking for a delightful treat that combines the best of two beloved desserts, this Apple Pie Cupcakes with Cream Cheese Frosting Recipe is absolutely worth making. It’s become one of my favorite ways to celebrate fall flavors anytime I want a cozy, sweet pick-me-up. Give it a try—you’ll enjoy how the familiar warmth of apple pie pairs with the softness of a cupcake and the tang of cream cheese frosting. I promise it’ll quickly become a crowd-pleaser in your home, just like it did in mine.

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