
These apple pie cupcakes with whipped cream topping bring together the warm spices of cinnamon and nutmeg with tender diced apples baked inside soft, moist cupcakes. They make a festive dessert that captures the feeling of homemade apple pie in a convenient handheld form perfect for holiday gatherings or cozy weekend treats. One autumn, my aunt took us apple picking at a local orchard, and I still remember the sweet aroma of cinnamon and apples filling the house as we baked homemade treats together. Topped with a swirl of lightly sweetened whipped cream and a dusting of cinnamon, each cupcake feels like a little celebration of fall and comfort.
I first made this recipe for a family gathering and the cupcakes disappeared almost instantly. They have since become a requested seasonal favorite that brings back memories of apple picking and baking together.
Ingredients
- Allpurpose flour: for a tender crumb choose unbleached for best texture
- Baking powder and baking soda: to give your cupcakes a light rise
- Salt: balances flavors in the batter
- Ground cinnamon: adds warm cozy spice that defines the fall flavor
- Unsalted butter for batter: provides richness use quality butter for best taste
- Granulated sugar: for sweetness and moisture
- Large eggs: to bind and enrich the batter room temperature helps with mixing
- Pure vanilla extract: enhances all the flavors with a hint of floral warmth
- Sour cream: adds moisture and a slight tang that keeps the cupcakes soft
- Whole milk: balances the batter for a perfect texture
- Honeycrisp apples: give a sweet crisp filling look for firm apples without bruises
- Unsalted butter for sauteing apples: for the filling and creating richness
- Light brown sugar: adds depth and caramel notes to the apple filling
- Ground nutmeg: complements the cinnamon with subtle earthiness
- Cornstarch: thickens the apple filling to keep it from running
- Heavy cream: whipped with powdered sugar and vanilla to top the cupcakes with light fluffy sweetness
- Powdered sugar: to sweeten and stabilize whipped cream
- Ground cinnamon for dusting: adds aroma and flair to the finished whipped cream
Instructions
- Prepare the Apple Pie Filling:
- In a medium skillet over medium heat melt the unsalted butter and add the peeled cored and diced apples along with light brown sugar ground cinnamon and nutmeg. Stir gently and cook for about five to seven minutes turning occasionally until the apples are tender while still holding their shape. Sprinkle cornstarch evenly over the mixture stir well and cook for an additional one to two minutes until the filling thickens noticeably. Transfer the filling to a bowl and let it cool completely to prevent soggy cupcakes later.
- Make the Cupcake Batter:
- Preheat your oven to 350 degrees Fahrenheit and line a 12 cup muffin tin with paper liners. In a medium bowl whisk together the flour baking powder baking soda salt and cinnamon ensuring the spices are well distributed. In a separate large bowl beat the softened butter with granulated sugar until the mixture is light and fluffy. Add the eggs one at a time beating thoroughly after each addition then stir in the vanilla extract. Beat in the sour cream gently until just combined. Alternate adding the dry flour mixture and whole milk into the wet ingredients starting and ending with the flour blend and mix only until just combined.
- Fill and Bake the Cupcakes:
- Spoon the cupcake batter into the liners filling each about two thirds full. Place a heaping teaspoon of the cooled apple pie filling into the center of each cupcake and carefully dollop a bit more batter on top of the apples just to cover them smoothing lightly. Bake in the preheated oven for eighteen to twenty two minutes. Test doneness by inserting a toothpick near the edge of a cupcake as it should come out clean or with a few moist crumbs but no batter. Cool the cupcakes in the pan for several minutes before transferring them to a wire rack to cool completely.
- Prepare the Whipped Cream Topping:
- Chill your mixing bowl and beaters in the fridge before whipping to help the cream whip faster and hold peaks. Pour the heavy cream into the chilled bowl and begin beating. As it starts to thicken slowly add the powdered sugar and vanilla extract and continue beating until the mixture holds soft peaks. Be careful not to overbeat or the cream will become grainy and start to separate.
- Finish and Present:
- When the cupcakes are fully cooled spoon or pipe generous swirls of whipped cream atop each one and use a fine sieve to dust a little ground cinnamon over the cream for a delicate finishing touch. Serve immediately for the fluffiest cream or refrigerate the cupcakes and add the cream topping shortly before serving for best texture.

The apple filling is my favorite part because it has the perfect balance of sweetness and spice. I remember once making these for a fall potluck where everyone kept guessing the secret filling and it was fun watching their faces when they bit into the cupcake and discovered the warm apple inside.
Storage Tips
Store leftover cupcakes in an airtight container in the refrigerator for up to three days. Keep whipped cream toppings covered or add fresh whipped cream just before serving to maintain peak fluffiness. Cupcakes without topping can be frozen for up to three months and should be thawed overnight in the fridge before serving.
Ingredient Substitutions
Use Greek yogurt in place of sour cream to add a bit of tang and tenderness while boosting protein. Granny Smith apples provide a tarter firmer filling that holds up well and adds a crisp contrast. Switch the whipped cream topping to coconut whipped cream for a dairy free option with a subtle tropical twist.
Serving Suggestions
These cupcakes pair beautifully with a drizzle of caramel sauce or a sprinkle of toasted pecans on top for extra texture and richness. Enjoy them alongside a warm chai tea or spiced apple cider to bring out the cozy flavors or for a lighter touch serve with a fresh fruit salad.

These apple pie cupcakes are a cozy seasonal treat that brings nostalgic fall flavors to any gathering. Make the filling ahead to save time and top with whipped cream just before serving for the best texture.
Common Questions About Recipes
- → Why do my cupcakes sink in the middle?
Sinking can occur from overmixing the batter or adding too much apple filling. Make sure the filling is fully cooled and use fresh leavening agents. Avoid opening the oven door during baking.
- → How can I prevent the whipped cream from wilting?
Add a tablespoon of instant pudding mix or dissolved gelatin while whipping. Keep cupcakes stored in the refrigerator and serve soon after topping.
- → Can I prepare the cupcakes ahead of time?
Yes, bake and fill the cupcakes up to a day in advance, storing them airtight. Whip and pipe the cream just before serving for best freshness.
- → What should I do if the apple filling is too runny?
Return the filling to heat and simmer a bit longer to reduce moisture. Add a bit more cornstarch mixed with water and cook until thickened.
- → How to keep the whipped cream topping stable outdoors?
Use stabilized whipped cream by adding pudding mix or gelatin. Keep cupcakes chilled until serving and transport in a cooler, avoiding direct sunlight.