Apple Pie Cupcakes

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Super moist and tender spiced cupcakes topped with an apple pie filling and frosted with a cream cheese whipped cream and streusel topping.

apple pie cupcakes with a bite taken out

Why You’ll Love These Apple Pie Cupcakes

  1. I used my favorite tried & true vanilla cupcake recipe except I used half light brown sugar instead and added cinnamon and nutmeg.
  2. Although these might take a little extra effort than your average cupcake, it’s totally worth it and easier than filling the cupcakes post baking.
  3. A moist cupcake topped with apple pie filling is an awesome twist on fall recipes that really goes well together, not to mention the cream cheese frosting that’s light as air!
  4. Perfect, easy to eat dessert for a small get together if you really want to impress your friends 🙂 

If you like these, you’ll love my Apple Cider Cupcakes, they have an apple cider base, apple cider frosting and apple cider caramel sauce. I also have plenty (my fav) of other apple recipes like my Iced Apple Crisp Macchiato, Apple Cider Donuts OR try my new Apple Ice Cream and serve it on a Dutch Apple Pie.

If you’re looking to pair these babies with other “fall-ey” cupcakes try my Pumpkin Cheesecake Cupcakes, S’mores Cupcakes, or Biscoff Cupcakes.

apple pie cupcakes with whipped cream frosting

Ingredients:

  • Butter: I like to use salted butter for my cupcakes, but you can also use unsalted butter, just add an extra ¼ tsp of salt to every cup of butter used. 
  • Oil: any neutral oil like vegetable oil, canola oil, grapeseed oil, etc. will work. 
  • Sugar: I usually use just granulated sugar for my cupcakes, but for this recipe I used ½ granulated and ½ light brown sugar. I also used light brown sugar for the streusel and filling and powdered sugar for the cream.
  • Vanilla: I use extract in this recipe but vanilla bean paste would work as well. 
  • Eggs: always use large, room temperature eggs. Place them in hot water for 5-10 minutes if they’re cold.
  • Flour: I usually use all-purpose flour for cakes but cupcakes are a different story. I use cake flour for most cupcakes. Although I do use all-purpose for the streusel here.
    • ​​I also HIGHLY recommend using a digital scale, as flour is almost always over measured. 
    • If you don’t have cake flour, you can substitute the cake flour for equal parts all-purpose flour – 1 Tbsp and then add 1 Tbsp cornstarch. It’s not a perfect substitute but will get the job done. To learn more about this, check out my ebook about ingredients. Use code BAKER for 60% off. 
  • Baking Powder: I just used baking powder for this recipe.
  • Salt: salt brings out the flavor in all baked goods.
  • Sour Cream: I use sour cream in almost all my cake and cupcake recipes. It brings and holds a lot of moisture into the cake. Plain greek yogurt or unsweetened regular yogurt also works.
  • Cream Cheese: I let it soften a bit and always use Philadelphia cream cheese.
  • Milk: any fat percentage of milk works, even plant based milk works.  
  • Heavy Whipping Cream: This gets whipped into the cream cheese frosting – I recommend 36-40% fat.
  • Apple: I used 3 medium apples cored, peeled, and diced. I like gala, fuji or honeycrisp but really any apple you like will work. Golden apples will get more soggy though.
  • Lemon: Whenever I bake with apples I like to coat them in lemon juice. This prevents them from getting brown super quick and brings out their natural tartness.
  • Spices: I use cinnamon and nutmeg in this recipe.
  • Cornstarch: Used to thicken the juices from the apples so that it gets more saucy and not runny.
apple pie cupcakes frosted with whipped cream frosting and topped with streusel topping

Step-by-Step Instructions

Apple Pie Filling

Step 1: Toss the apples with the lemon juice, cinnamon, nutmeg, salt and sugar.

apples sliced before cooking

Step 2: Melt butter in a saucepan and add the apple mixture. Cook for about 7 minutes, until the apples start to feel a little more tender.

Step 3: Remove about 2 Tbsp of the liquid into the bowl and mix it with the cornstarch then add it back to the pot cooking 1-2 mins until it thickens.

apple pie cupcake filling

Spice Cupcakes

Step 1: Whisk together the cake flour, baking powder, salt, spices and sugars.

Step 2: Add the oil and butter to the dry ingredients and continue mixing, just until it’s all crumbly.

dry ingredients mixed with butter and oil.

Step 3: Add the egg and vanilla and continue mixing until it’s smooth.

eggs added to the cupcake batter

Step 4: Add the sour cream and stream the milk in, scrape the edges while mixing until smooth.

finished cupcake batter

Step 5: Fill each cupcake liner about ⅔ full and then top with the apple pie filling.

apple pie topping on top of cupcakes before baking

Step 6: Bake for 22-25 minutes, remove and let them cool in the pan for 10 minutes before fully removing to a cooling rack.

apple pie topping on top of cupcakes after baking

Streusel Topping

Step 1: Melt the butter and add the sugar, cinnamon and salt. Mix until it’s well combined.

Step 2: Add the flour, mix gently, then bake for 5 minutes on a cookie sheet.

Step 3: Remove pan, toss the streusel, then repeat 5 minute bake time. Do this 3-4 rounds until the streusel has browned and is crispy. Then set aside to cool.

finished streusel

Cream Cheese Whipped Cream

Step 1: Place the room temperature cream cheese in the bowl and beat at medium speed for a minute until it’s creamy.

Step 2: Add the powdered sugar, vanilla and salt and beat again until it’s smooth and combined.

cream cheese mixed with sugar and vanilla

Step 3: Stream in heavy whipping cream and beat until it’s thickened like fluffy whipped cream.

finished frosting

Step 4: Frost the cooled cupcakes and then roll the sides of the frosting in the cooled streusel or just sprinkle on top. 

finished apple pie cupcakes

Expert Tips On Getting Perfect Cupcakes

There’s a few things that can make it or break it with these cupcakes. 

  • Don’t swap ingredients unless I mentioned them in the ingredient section above.
  • Don’t reduce the sugar. I know a lot of people do that for some recipes but it alters the texture not just the flavor.
  • Weigh your ingredients with a digital scale 
  • Weigh the batter for each cupcake with a digital scale. I just place the cupcake pan on the scale with the liners and measure out 45 grams for each cupcake and 20-25 grams of apple pie filling. 
  • Use a light colored stainless steel muffin tin for a more even bake.
apple pie cupcakes with a bite taken out

Frequently Asked Questions

What other toppings can I use on my cupcakes?

You can make a streusel out of leftover pie crust, crushing it and adding it on top. If you want to skip the streusel altogether you can drizzle on some caramel sauce over the frosting like I did for my Apple Cider Cupcakes or Pumpkin Cupcakes.
Or a graham cracker dusting like I did for my Pumpkin Cheesecake Cupcakes. 

Can I make these cupcake dairy free?

You can use dairy free butter, dairy free milk, cream cheese and heavy cream to make these. I don’t have much experience with dairy free cream cheese so whatever one you like the taste of will probably be best for you. If the cream is too runny, reduce the amount of heavy cream or increase the amount of powdered sugar. 

Can I make these cupcakes gluten-free?

I have not tested my cupcake recipes, but all my cake and cookie recipes work well with a 1:1 gluten-free flour like Bob’s Red Mill and King Arthur Flour. 

How do I know when cupcakes are done baking?

It’s kind of difficult to tell with these cupcakes so I just stuck a toothpick into one of the side areas where that wasn’t covered in apple pie. 

finished apple pie cupcakes with streusel topping

How To Store Apple Pie Cupcakes

Serve the cupcakes fresh or refrigerate them for a few days.

To refrigerate, make sure to cover the cupcakes with a cake dome or store them in an airtight container for up to a week.

To freeze it, place them in an airtight container and then place the container in an airtight bag. Thaw at room temperature before serving.  

spice cupcakes with apple pie filling and cream cheese frosting and streusel topping

Thanks so much for reading today’s post, if you have any questions just comment down below. 

If you make these apple pie cupcakes, I would love it if you left a star rating for it in the recipe card. 

As always, have a blessed day and happy baking!

Love, B

apple pie cupcakes with a bite taken out

Apple Pie Cupcakes

Bernice Baran
Apple pie cupcakes are a super moist and tender spiced cupcakes topped with an apple pie filling and frosted with a cream cheese whipped cream and streusel topping.
4.89 from 9 votes
Print Recipe Pin Recipe
Prep Time 1 hour
Cook Time 23 minutes
Additional Time 1 hour
Total Time 2 hours 23 minutes
Course Cupcakes
Cuisine American
Servings 12 cupcakes
Calories 433 kcal

Equipment

Ingredients
  

Apple Pie Filling

  • 3 medium apples 10oz/275g after it's cored, peeled and diced
  • 2 Tbsp (30mL) fresh lemon juice (1/2 large lemon)
  • ½ tsp ground cinnamon
  • 1/4 cup (50g) light brown sugar, lightly packed
  • 2 Tbsp (28g) salted butter
  • 1 Tbsp (10g) cornstarch

Spice Cupcakes

  • 1 1/2 cup (172g) cake flour spooned and leveled
  • 1 1/2 tsp baking powder
  • 1/4 tsp fine sea salt
  • 2 tsp ground cinnamon
  • 1 tsp ground nutmeg
  • 1/2 cup (100g) granulated sugar
  • 1/2 cup (100g) light brown sugar lightly packed
  • 1/4 cup (60mL) canola oil
  • 1/4 cup (56g) salted butter room temperature
  • 1 large egg room temperature
  • 1 tsp pure vanilla extract
  • 1/2 cup (113g) sour cream
  • 1/3 cup (80mL) whole milk room temperature

Streusel Topping

  • 1/2 cup (60g) all-purpose flour spooned and leveled
  • 2 Tbsp (25g) light brown sugar
  • 2 Tbsp (28g) salted butter melted
  • 1/2 tsp ground cinnamon
  • tiny pinch fine sea salt

Cream Cheese Whipped Cream

  • 2 oz (1/4 brick) cream cheese room temperature
  • 1 cup (120g) powdered sugar spooned and leveled
  • 1 tsp vanilla extract
  • tiny pinch salt
  • 1 cup (8oz) heavy whipping cream cold

Instructions
 

Apple Pie Filling

  • In a small bowl, toss the apples with the lemon juice, cinnamon, nutmeg, salt and sugar.
    3 medium apples, 2 Tbsp (30mL) fresh lemon juice (1/2 large lemon), ½ tsp ground cinnamon, 1/4 cup (50g) light brown sugar, lightly packed
  • Place the butter in a small or medium saucepan, over medium heat. Once the butter is melted, add the apple mixture and cook over medium heat for about 7 minutes, until the apples start to feel a little more tender. 
    2 Tbsp (28g) salted butter
  • Remove about 2 Tbsp of the liquid into the bowl and mix it with the cornstarch to make a slurry. Add the slurry to the pot with the apples and cook for another 1-2 minutes until it thickens.  
    1 Tbsp (10g) cornstarch

Spice Cupcakes

  • Preheat the oven to 350F/177C convection (325F/163C conventional) and line 13 muffin tins with cupcake liners (preferably a light colored pan).
  • In a medium bowl, whisk together the cake flour, baking powder, salt, spices and sugars until they're evenly distributed (whisk well).
    1 1/2 cup (172g) cake flour, 1 1/2 tsp baking powder, 1/4 tsp fine sea salt, 2 tsp ground cinnamon, 1 tsp ground nutmeg, 1/2 cup (100g) granulated sugar, 1/2 cup (100g) light brown sugar
  • Add the oil and butter to the dry ingredients and beat together until they're combined.
    1/4 cup (60mL) canola oil, 1/4 cup (56g) salted butter
  • Add the egg and vanilla extract and paste and mix until they're fully combined.
    1 large egg, 1 tsp pure vanilla extract
  • Add the sour cream and turn the mixer to low speed, while streaming the milk in. Scrape the edge of the bowl and mix just until the cupcake batter is smooth.
    1/2 cup (113g) sour cream, 1/3 cup (80mL) whole milk
  • Fill each cupcake liner about 2/3 full, about 45 grams of batter per cupcake.* You should have enough for 15 cupcakes.
  • Top with the apple pie filling, about 20-25 grams per cupcake, and bake for 22-25 minutes. If you press on the cupcake gently, it should bounce back. You can also insert a toothpick through the side to make sure the batter is baked.
  • Remove them from the oven and let them cool in the cupcake pan for 10 minutes, then move them to a cooling rack. Allow the cupcakes to cool completely before frosting.

Streusel Topping

  • In a small bowl, melt the butter and add the sugar, cinnamon and salt. Mix until it's well combined.
    2 Tbsp (25g) light brown sugar, 2 Tbsp (28g) salted butter, 1/2 tsp ground cinnamon, tiny pinch fine sea salt
  • Add the flour and mix gently just until it crumbles into chunks. Place the streusel on a baking sheet and bake for 5 minutes.
    1/2 cup (60g) all-purpose flour
  • Remove the pan from the oven and then use a fork or a spatula to toss the streusel around. Bake for another 5 minutes. Repeat the process again, baking for a total of 15-20 minutes for 3-4 rounds, until the streusel has browned and is crispy.
  • Remove from the oven and set aside to cool completely before adding to the cupcakes.

Cream Cheese Whipped Cream

  • Place the room temperature cream cheese in the bowl of a stand mixer (or a large bowl with a hand mixer) and beat at medium speed for a minute until it's creamy.
    2 oz (1/4 brick) cream cheese
  • Add the powdered sugar, vanilla and salt and beat again at low-medium speed, just until they're smooth and combined.
    1 cup (120g) powdered sugar, 1 tsp vanilla extract, tiny pinch salt
  • Turn the mixer to low speed and stream in the heavy whipping cream. Once it's all added, turn the mixer up to medium-high speed and beat for 1-2 minutes until it's thickened like fluffy whipped cream. Don't over-beat.
    1 cup (8oz) heavy whipping cream
  • Use the frosting to frost the cupcakes and then roll the sides of the frosting in the cool streusel.
  • Serve immediately or store refrigerated.

Nutrition

Serving: 1gCalories: 433kcalCarbohydrates: 45gProtein: 5gFat: 26gSaturated Fat: 13gPolyunsaturated Fat: 12gCholesterol: 125mgSodium: 136mgSugar: 32g
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