I’m sharing my Cinnamon Apple Pie Cupcakes that tuck a spiced apple pie filling into each tender cake, and I’ll reveal the simple trick I use to keep the filling intact and the crumb delightfully light.

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I’ve been making these Apple Pie Filled Cupcakes so much lately I forget people ever ate plain cupcakes. If you love apples you’re gonna stan this take on a classic, all the warm spice without being cloying.

I stuff each one with a sneaky apple pie center and the batter carries a cozy note of ground cinnamon that just sings with the filling. For me the best part is the tangy cream cheese finish that keeps things interesting, not just sweet.

They’re perfect for Thanksgiving or any fall day when you want dessert that feels a little extra. Try one, you won’t regret it.

Ingredients

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Apples add fiber and natural sweetness, a little tartness if you use granny smith.
Flour gives structure and carbs, so cupcakes hold together and feel bready.
Butter brings richness, fat and moistness, helps flavors taste more rounded.
Brown sugar gives molassesy sweetness and slight chew, keeps things caramelized.
Cream cheese adds tang and creamy texture, balances sweet frosting well.
Cinnamon adds warm spice and aroma, makes them smell homestyle and cozy.
Eggs give protein, structure and help bind, also add tender crumb.
Sour cream brings tang and moisture, Greek yogurt adds protein and thickness.

Ingredient Quantities

1 1/2 cups (190 g) all-purpose flour

1 tsp baking powder

1/2 tsp baking soda

1/2 tsp salt

1 1/2 tsp ground cinnamon

1/4 tsp ground nutmeg

1/4 tsp ground ginger

1/2 cup (113 g) unsalted butter, softened

3/4 cup (150 g) granulated sugar

1/4 cup (50 g) packed light brown sugar

2 large eggs

1 tsp vanilla extract

1/2 cup (120 g) sour cream or plain Greek yogurt

1/4 cup (60 ml) milk

1 1/2 cups (about 2 medium) diced apples

For the apple pie filling 1 cup (about 1 medium) diced apples

2 tbsp packed light brown sugar

1 tsp ground cinnamon

1 tsp lemon juice

1 tsp cornstarch

1 tbsp unsalted butter

Pinch salt

For the frosting 4 oz (113 g) cream cheese, softened

1/2 cup (113 g) unsalted butter, softened

2 cups (240 g) powdered sugar

1 tsp vanilla extract

1/2 tsp ground cinnamon

Pinch salt

1 to 2 tbsp milk or heavy cream

How to Make this

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1. Preheat oven to 350 F (175 C) and line a 12-cup muffin tin with liners or lightly grease the cups.

2. Make the apple pie filling: in a small saucepan combine 1 cup diced apples, 2 tbsp packed light brown sugar, 1 tsp ground cinnamon, pinch of salt and 1 tsp lemon juice. Mix 1 tsp cornstarch with about 1 tbsp cold water to make a slurry, stir it in, add 1 tbsp unsalted butter and cook over medium heat until the apples are tender and the mixture thickens, about 3 to 5 minutes. Remove from heat and let cool completely.

3. Whisk the dry batter ingredients: 1 1/2 cups (190 g) all purpose flour, 1 tsp baking powder, 1/2 tsp baking soda, 1/2 tsp salt, 1 1/2 tsp ground cinnamon, 1/4 tsp ground nutmeg and 1/4 tsp ground ginger. Set aside.

4. Cream the butter and sugars: in a bowl beat 1/2 cup (113 g) softened unsalted butter with 3/4 cup (150 g) granulated sugar and 1/4 cup (50 g) packed light brown sugar until light and fluffy. Beat in 2 large eggs one at a time, then stir in 1 tsp vanilla extract.

5. Combine wet and dry: whisk together 1/2 cup (120 g) sour cream or plain Greek yogurt and 1/4 cup (60 ml) milk. Add the dry mix to the creamed mixture in three additions, alternating with the sour cream mixture, beginning and ending with the dry. Mix only until just combined, dont overmix or the cupcakes get tough.

6. Prep the apples in the batter: toss 1 1/2 cups (about 2 medium) diced apples with a teaspoon of the reserved flour from step 3 or a pinch of flour so they dont sink, then gently fold them into the batter.

7. Fill and stuff: spoon batter into liners about halfway, add about 1 tsp to 1 tbsp of the cooled apple pie filling into the center of each (depending how much filling you like), then top with more batter until cups are about two thirds full. Tap the pan lightly to remove big air bubbles.

8. Bake for 18 to 22 minutes, or until a toothpick inserted in the cake part comes out clean or with just a few moist crumbs (a little apple may stick). Let cupcakes cool in the tin 5 minutes then transfer to a wire rack to cool completely before frosting.

9. Make the frosting: beat 4 oz (113 g) softened cream cheese with 1/2 cup (113 g) softened unsalted butter until smooth. Gradually add 2 cups (240 g) powdered sugar, then beat in 1 tsp vanilla extract, 1/2 tsp ground cinnamon and a pinch of salt. Add 1 to 2 tbsp milk or heavy cream to reach a spreadable or pipeable consistency. Chill briefly if it gets too soft.

10. Assemble and store: frost cooled cupcakes, dollop a little extra apple filling on top if you want and sprinkle a pinch of cinnamon. Store in the fridge because of the cream cheese frosting, they keep well 3 to 4 days. Enjoy, these are best at room temp after chilling.

Equipment Needed

1. 12-cup muffin tin, lined or greased so the cupcakes dont stick
2. Paper cupcake liners or a little nonstick spray for the cups
3. Medium saucepan for the apple pie filling
4. Mixing bowls (one large for batter, one small for wet ingredients)
5. Electric hand mixer or stand mixer to cream butter and sugar (you can whisk by hand but it takes longer)
6. Whisk and a rubber spatula for folding and scraping the bowl
7. Measuring cups and spoons for dry and wet ingredients
8. Paring knife and cutting board to dice the apples
9. Wire cooling rack so the cupcakes cool evenly before frosting

FAQ

How many cupcakes does this recipe make and what temp and time should I bake them at?

Yields about 12 standard cupcakes. Bake at 350°F (175°C) for 18 to 22 minutes. Start checking at 16 minutes, ovens differ, and a toothpick should come out with a few moist crumbs not wet batter.

Do I need to peel the apples and which apples are best?

You can leave the peel on if you like more texture, but peeling gives a smoother bite. Good choices are Honeycrisp, Gala, Fuji for sweetness or Granny Smith if you want tang. Dice medium small so they cook and fold into the batter evenly.

My cupcakes got soggy from the apple filling before, how do I stop that?

Toss diced apples with a little cornstarch or flour before folding into batter, and make sure the apple pie filling is thick and cooled before adding to cupcakes. Don’t overfill the center and bake on the middle rack so they cook through.

Can I swap the sour cream for something else?

Yes use plain Greek yogurt 1 to 1. If you only have low fat yogurt add a teaspoon of oil or a splash more milk to keep them moist. Buttermilk also works, use same amount.

How do I store or freeze the cupcakes?

Unfrosted cupcakes keep at room temp for 1 to 2 days in an airtight container, or in the fridge up to 3 days. Frosted cupcakes should be refrigerated up to 3 days. For longer storage freeze unfrosted cupcakes wrapped tight for up to 3 months, thaw overnight in the fridge and frost when ready. You can also freeze frosting in a small container and thaw before piping.

My cupcakes turned out dense, what went wrong?

Most common reasons are overmixing the batter, measuring flour too tightly, or old baking powder/soda. Use the weight measures if you can, mix just until combined, and make sure your leaveners are fresh.

Apple Pie Cupcakes Recipe Substitutions and Variations

All-purpose flour: swap for whole wheat pastry flour 1:1 for a nuttier flavor, it’ll be a bit denser but still good; or use a gluten-free cup-for-cup blend 1:1 (make sure it has xanthan gum).
Unsalted butter: use solid coconut oil 1:1 by weight for a dairy-free option, note it may add a mild coconut taste; or use a neutral vegetable oil 1:1 and skip the creaming step since texture changes.
Eggs: replace each egg with a flax egg (1 tbsp ground flax + 3 tbsp water, let sit 5 min), it’s great for binding but cupcakes will be a tad denser and may not rise as much.
Cream cheese (frosting): swap with mascarpone 1:1 for an even silkier, milder frosting; or use vegan cream cheese 1:1 if avoiding dairy, you might need 1 to 2 tbsp more powdered sugar to firm it up.

Pro Tips

– Get everything to room temp and measure flour right. Cold eggs or butter makes the batter seize up so your cupcakes can be dense, not fluffy. And spoon your flour into the measuring cup then level it off with a knife instead of scooping straight from the bag, you’ll avoid packing too much flour.

– Keep your apple bits from sinking or watering the batter. Dice them small, toss them with a little of the dry flour like the recipe says, and use a mix of tart and sweet apples so the texture and flavor balance. For the filling, cook it until most of the liquid is gone and let it cool completely before stuffing, otherwise it bleeds into the cake.

– Dont overmix the batter, especially after you add the sour cream. Mix just until you cant see streaks of flour. If you overwork it the cupcakes get tough. Fold the apples in gently with a spatula, scrape the sides and bottom so everything is evenly combined.

– Chill the frosting briefly if it gets too soft and always frost fully cooled cupcakes. Store in the fridge because of the cream cheese, but take them out about 20 to 30 minutes before serving so the frosting softens and the flavors open up. If you want a little crunch, sprinkle coarse sugar or chopped nuts on top right before serving.

Apple Pie Cupcakes Recipe

Recipe by Sammy Hunter

0.0 from 0 votes

Servings

servings

Calories

423

kcal

Equipment: 1. 12-cup muffin tin, lined or greased so the cupcakes dont stick
2. Paper cupcake liners or a little nonstick spray for the cups
3. Medium saucepan for the apple pie filling
4. Mixing bowls (one large for batter, one small for wet ingredients)
5. Electric hand mixer or stand mixer to cream butter and sugar (you can whisk by hand but it takes longer)
6. Whisk and a rubber spatula for folding and scraping the bowl
7. Measuring cups and spoons for dry and wet ingredients
8. Paring knife and cutting board to dice the apples
9. Wire cooling rack so the cupcakes cool evenly before frosting

Ingredients

1 1/2 cups (190 g) all-purpose flour
1 tsp baking powder
1/2 tsp baking soda
1/2 tsp salt
1 1/2 tsp ground cinnamon
1/4 tsp ground nutmeg
1/4 tsp ground ginger
1/2 cup (113 g) unsalted butter, softened
3/4 cup (150 g) granulated sugar
1/4 cup (50 g) packed light brown sugar
2 large eggs
1 tsp vanilla extract
1/2 cup (120 g) sour cream or plain Greek yogurt
1/4 cup (60 ml) milk
1 1/2 cups (about 2 medium) diced apples
For the apple pie filling 1 cup (about 1 medium) diced apples
2 tbsp packed light brown sugar
1 tsp ground cinnamon
1 tsp lemon juice
1 tsp cornstarch
1 tbsp unsalted butter
Pinch salt
For the frosting 4 oz (113 g) cream cheese, softened
1/2 cup (113 g) unsalted butter, softened
2 cups (240 g) powdered sugar
1 tsp vanilla extract
1/2 tsp ground cinnamon
Pinch salt
1 to 2 tbsp milk or heavy cream

Directions

Preheat oven to 350 F (175 C) and line a 12-cup muffin tin with liners or lightly grease the cups.
Make the apple pie filling: in a small saucepan combine 1 cup diced apples, 2 tbsp packed light brown sugar, 1 tsp ground cinnamon, pinch of salt and 1 tsp lemon juice. Mix 1 tsp cornstarch with about 1 tbsp cold water to make a slurry, stir it in, add 1 tbsp unsalted butter and cook over medium heat until the apples are tender and the mixture thickens, about 3 to 5 minutes. Remove from heat and let cool completely.
Whisk the dry batter ingredients: 1 1/2 cups (190 g) all purpose flour, 1 tsp baking powder, 1/2 tsp baking soda, 1/2 tsp salt, 1 1/2 tsp ground cinnamon, 1/4 tsp ground nutmeg and 1/4 tsp ground ginger. Set aside.
Cream the butter and sugars: in a bowl beat 1/2 cup (113 g) softened unsalted butter with 3/4 cup (150 g) granulated sugar and 1/4 cup (50 g) packed light brown sugar until light and fluffy. Beat in 2 large eggs one at a time, then stir in 1 tsp vanilla extract.
Combine wet and dry: whisk together 1/2 cup (120 g) sour cream or plain Greek yogurt and 1/4 cup (60 ml) milk. Add the dry mix to the creamed mixture in three additions, alternating with the sour cream mixture, beginning and ending with the dry. Mix only until just combined, dont overmix or the cupcakes get tough.
Prep the apples in the batter: toss 1 1/2 cups (about 2 medium) diced apples with a teaspoon of the reserved flour from step 3 or a pinch of flour so they dont sink, then gently fold them into the batter.
Fill and stuff: spoon batter into liners about halfway, add about 1 tsp to 1 tbsp of the cooled apple pie filling into the center of each (depending how much filling you like), then top with more batter until cups are about two thirds full. Tap the pan lightly to remove big air bubbles.
Bake for 18 to 22 minutes, or until a toothpick inserted in the cake part comes out clean or with just a few moist crumbs (a little apple may stick). Let cupcakes cool in the tin 5 minutes then transfer to a wire rack to cool completely before frosting.
Make the frosting: beat 4 oz (113 g) softened cream cheese with 1/2 cup (113 g) softened unsalted butter until smooth. Gradually add 2 cups (240 g) powdered sugar, then beat in 1 tsp vanilla extract, 1/2 tsp ground cinnamon and a pinch of salt. Add 1 to 2 tbsp milk or heavy cream to reach a spreadable or pipeable consistency. Chill briefly if it gets too soft.
Assemble and store: frost cooled cupcakes, dollop a little extra apple filling on top if you want and sprinkle a pinch of cinnamon. Store in the fridge because of the cream cheese frosting, they keep well 3 to 4 days. Enjoy, these are best at room temp after chilling.

Notes

Below you’ll find my best estimate of this recipe’s nutrition facts. Treat the numbers as a guide rather than a rule—great food should nourish both body and spirit. Figures are approximate, and the website owner assumes no liability for any inaccuracies in this recipe.