As the air turns crisp and the leaves begin to crunch underfoot, I can’t help but find myself daydreaming about the warm, spiced scents of the season wafting from my kitchen. Enter these delightful Apple Pie Cupcakes! Soft and fluffy, they are filled with a homemade apple compote that echoes the classic flavors of your grandmother’s apple pie. This cozy fall treat is topped with a heavenly cinnamon cream cheese frosting, making them a perfect indulgence for any gathering. Not only are these cupcakes a crowd-pleaser, but they’re also quick to whip up, allowing you to enjoy more time with loved ones. Who can resist the allure of a dessert that combines two beloved classics into one? Are you ready to dive into the world of apple-themed baking and fill your home with the spirit of fall?
Why Are These Cupcakes a Must-Try?
Irresistible Flavor: These Apple Pie Cupcakes blend warm, spiced apple compote with a velvety cinnamon cream cheese frosting, creating an explosion of flavor that feels like a hug in dessert form.
Easy to Make: With simple, pantry-friendly ingredients, you don’t need to be a baking pro to whip these up! They come together quickly, making them perfect for any day of the week.
Perfect for Fall Gatherings: Whether you’re hosting a cozy get-together or just want to enjoy seasonal treats, these muffins will impress your guests. Pair them with a scoop of vanilla ice cream for an extra touch!
Customization Galore: Feel free to switch up the frosting or even the fillings! Want to experiment? Try adding pear or pumpkin for a delightful twist. Don’t forget to check out my Salted Caramel Apple recipe for another scrumptious option!
Fun for Everyone: Kids and adults alike love these delightful cupcakes, making them a hit at family gatherings. They bring a taste of nostalgia with a modern touch.
Apple Pie Cupcake Ingredients
For the Apple Compote
• Tart Apples – Fresh apples (4 small, peeled, cored, finely diced) provide the primary apple flavor; substitute with firm apples like Granny Smith or Honeycrisp for tartness.
• Brown Sugar – (30 g) Sweetens with a hint of caramel flavor; use coconut sugar for a richer taste.
• Cornstarch – (2 teaspoons) Thickens the apple filling; substitute with arrowroot powder for a gluten-free option.
• Ground Cinnamon – (1 teaspoon + 1 teaspoon) Offers warmth and ties the flavors together; use nutmeg for a spicier taste.
• Water – (50 g) Helps cook the apples until tender; can be omitted if the apples are juicy enough.
For the Cupcakes
• Cake Flour – (185 g) Keeps the cupcakes tender and light; substitute with all-purpose flour but expect a denser texture.
• Baking Powder – (1 ½ teaspoons) Provides leavening to create fluffy cupcakes.
• Salt – (½ teaspoon) Balances sweetness and enhances flavor.
• Unsalted Butter – (115 g + 60 g) Adds moisture and richness; use dairy-free butter as a substitute.
• Granulated Sugar – (200 g) Sweetens the cupcake mixture; try using a sugar substitute like erythritol for a low-calorie version.
• Eggs – (3 large, room temperature) Provide structure and moisture; aquafaba can be used as a vegan substitute (approximately 9 tablespoons).
• Vanilla Extract – (1 teaspoon) Enhances overall flavor; opt for pure vanilla extract for the best taste.
• Milk – (150 g) Adds moisture; substitute with a plant-based milk for a dairy-free version.
For the Frosting
• Cream Cheese – (125 g) Creamy base for frosting; use a vegan cream cheese alternative for dairy-free frosting.
• Powdered Sugar – (75 g) Sweetens and thickens the frosting; use erythritol powdered sugar for a low-sugar option.
These Apple Pie Cupcakes promise both flavor and comfort as you dive into fall baking!
Step‑by‑Step Instructions for Apple Pie Cupcakes
Step 1: Prepare Apple Filling
In a medium saucepan over medium heat, combine the finely diced tart apples, brown sugar, cornstarch, ground cinnamon, and water. Cook for about 10–12 minutes, stirring occasionally, until the apples are tender and most of the liquid has evaporated. Once done, remove from heat and allow the apple compote to cool completely before using it to fill your Apple Pie Cupcakes.
Step 2: Preheat Oven
Preheat your oven to 350°F (175°C), ensuring it’s properly heated for even baking. Meanwhile, line a cupcake pan with cupcake liners to prevent sticking and make cleanup easier. This preparation step is essential for achieving perfectly baked Apple Pie Cupcakes that rise beautifully.
Step 3: Mix Dry Ingredients
In a large mixing bowl, whisk together the cake flour, baking powder, additional ground cinnamon, and salt until evenly combined. This mixture helps create tender and fluffy cupcakes, so make sure there are no lumps. Set the bowl aside while you work on the wet ingredients, keeping the dry ingredients organized for easy incorporation.
Step 4: Beat Wet Ingredients
In another bowl, cream the softened unsalted butter until light and fluffy, about 2-3 minutes. Gradually add the granulated sugar, continuing to beat for an additional 2 minutes. Next, incorporate the eggs, one at a time, mixing well after each addition, and then stir in the vanilla extract. This combination ensures your Apple Pie Cupcakes are rich and flavorful.
Step 5: Combine Mixtures
Gently fold the dry ingredients into the wet mixture, alternating with the milk. Start and end with the dry ingredients, mixing just until everything is combined and smooth. Be careful not to overmix, as this could lead to denser cupcakes. The batter should be velvety and ready to fill your cupcake liners with the taste of apple goodness.
Step 6: Fill Liners
Using a scoop or spoon, fill each cupcake liner about two-thirds full with batter. This allows space for the cupcakes to rise without overflowing. With the sweet aroma of apple pie flavor in the air, prepare to bake these delightful Apple Pie Cupcakes to perfection.
Step 7: Bake
Place the filled cupcake pan in the preheated oven and bake for 18–20 minutes, or until a toothpick inserted into the center comes out clean. The tops should be lightly golden and spring back when gently pressed. Allow the cupcakes to cool in the pan for 5 minutes before transferring them to a wire rack to cool completely.
Step 8: Make Frosting
In a mixing bowl, beat the softened cream cheese and remaining butter until smooth and creamy. Gradually add the powdered sugar, cinnamon, and vanilla extract, mixing until well combined and thick enough to hold its shape. This luscious cinnamon cream cheese frosting will elevate your Apple Pie Cupcakes to a new level of deliciousness.
Step 9: Assemble Cupcakes
Once the cupcakes are completely cooled, use a small knife to scoop out a portion from the center of each cupcake. Fill the center with the cooled apple compote, then generously pipe the frosting on top. This final step brings your Apple Pie Cupcakes to life, creating a delightful surprise inside and wrapping them in creamy goodness.
What to Serve with Apple Pie Cupcakes
Looking for the perfect accompaniment to your delightful cupcakes that will elevate your fall gathering?
- Vanilla Ice Cream: A scoop of creamy vanilla ice cream adds a rich, cold contrast to the warm apple flavors of the cupcakes.
- Bourbon Caramel Sauce: Drizzle a touch of this sweet, indulgent sauce over the cupcakes for an extra layer of flavors, emphasizing the warmth of the spices.
- Spiced Chai Tea: Serve with warm spiced chai tea to echo the warm flavors in the cupcakes, creating a cozy atmosphere for any gathering.
- Pecan Pie Bars: Pairing these cupcakes with nutty, sweet pecan pie bars makes for a beautiful fall dessert table that balances flavors and textures.
- Pumpkin Spice Latte: Complete your dessert experience with a rich pumpkin spice latte, enhancing the cozy vibe and inviting seasonal flavors.
- Fresh Fruit Salad: A light, refreshing fruit salad can provide a bright, juicy contrast that cleanses the palate after enjoying your cupcakes.
- Maple Glazed Doughnuts: For the sweet-toothed among us, serving these doughnuts alongside adds a delightful variety of textures and flavors to your dessert spread.
- Cinnamon Hot Chocolate: For an indulgent experience, offer a cup of rich cinnamon hot chocolate that matches the cupcake’s cozy flavors perfectly.
How to Store and Freeze Apple Pie Cupcakes
Fridge: Store the cupcakes in an airtight container for up to 3 days to keep them fresh. This will help maintain their moisture and flavor.
Freezer: For longer storage, freeze the cupcakes for up to 1 month. Place them in a single layer in a freezer-safe container or wrap individually in plastic wrap before adding to the container.
Thawing: When ready to enjoy, simply thaw the Apple Pie Cupcakes at room temperature for about 30 minutes. This will ensure they taste just as delightful as when freshly made!
Reheating: If you prefer them warm, quickly pop them in the microwave for about 10-15 seconds to revitalize their fluffy texture before serving.
Expert Tips for Apple Pie Cupcakes
- Room Temperature Eggs: Ensure eggs are at room temperature to help them incorporate smoothly into the batter, creating a fluffier cupcake.
- Don’t Overmix: Mix the batter just until combined to avoid dense Apple Pie Cupcakes; overmixing can lead to unwanted gluten development.
- Cool Completely: Allow the cupcakes to cool completely before filling and frosting. This prevents the frosting from melting and maintains a beautiful presentation.
- Use a Piping Bag: To achieve a professional look, use a piping bag for the frosting. It’s not only easier but also adds a charming touch!
- Taste Test the Compote: Adjust the sweetness of the apple compote to your liking. A little extra cinnamon or sugar can enhance flavor, ensuring your cupcakes are irresistibly delicious.
Make Ahead Options
These Apple Pie Cupcakes are perfect for meal prep, allowing you to enjoy them effortlessly during your busy week! You can prepare the apple compote up to 3 days in advance—just store it in an airtight container in the refrigerator to maintain freshness. The cupcake batter can also be made ahead and refrigerated for up to 24 hours; just give it a gentle stir before filling the liners and baking. When it comes time to serve, bake the cupcakes fresh for best quality, and avoid overfilling the liners to prevent overflow. Finish them off by frosting with the cinnamon cream cheese frosting just before serving, ensuring they taste just as delicious as when made fresh!
Apple Pie Cupcakes Variations & Substitutions
Feel free to get creative with these Apple Pie Cupcakes—customizing is half the fun! Let your imagination run wild and savor the delightful possibilities.
- Gluten-Free: Use a gluten-free flour blend in place of cake flour, allowing everyone to enjoy these treats.
- Vegan: Swap out the eggs for aquafaba and use dairy-free butter and vegan cream cheese in the frosting for a compassionate twist.
- Nutty Crunch: Add chopped pecans or walnuts to the apple compote for a delightful texture and nutty flavor that elevates your cupcakes.
- Spice It Up: Experiment with your favorite spices like cardamom or ginger for a warm kick that will take your cupcakes to the next level.
- Different Fruit: Replace the apple filling with pears or seasonal pumpkin to create a new favorite. Pear Pie Cupcakes? Yes, please!
- Chocolate Lovers: Incorporate cocoa powder into half of the batter for a marble effect; this chocolate-apple combination is enchanting and rich.
- Cinnamon Roll Twist: Drizzle a cinnamon sugar mixture on top of the cupcakes before baking to create a sweet, caramelized crust, reminiscent of a morning treat.
Want more delicious ideas? Check out my Honeycrisp Apple Broccoli salad for a fresh take or try these Salted Caramel Apple bars for dessert inspirations that keep the fall spirit alive.
Apple Pie Cupcakes Recipe FAQs
What kind of apples should I use for the apple compote?
For the best flavor, I recommend using tart apples like Granny Smith or Honeycrisp. They provide the perfect balance of sweetness and tartness, reminiscent of traditional apple pie. If you’re in the mood to experiment, any firm apple variety will work, but avoid overly soft ones.
How long can I store my Apple Pie Cupcakes and how should I do it?
You can store the cupcakes in an airtight container in the fridge for up to 3 days. This will help keep them moist and delicious! If you find yourself with leftovers, I often refrigerate them to maintain their flavor.
Can I freeze Apple Pie Cupcakes? If so, how?
Absolutely! To freeze, place the cupcakes in a single layer in a freezer-safe container or wrap them individually in plastic wrap. This method protects them from freezer burn. They can be stored frozen for up to 1 month. When you’re ready to enjoy them, simply thaw at room temperature for about 30 minutes for best results.
What should I do if my cupcake batter seems too thick?
If your batter is thick, you can add a splash of milk—just a tablespoon or so—to loosen it up. Mix gently to avoid overworking the batter, which can make the cupcakes dense. The finished texture should be smooth and pourable, so don’t hesitate to adjust as needed!
Are these cupcakes suitable for those with dietary restrictions?
Yes! To make them dairy-free, substitute regular butter and cream cheese with their dairy-free alternatives. For a vegan option, use aquafaba in place of eggs and ensure your cream cheese is vegan. If you have a gluten intolerance, swapping cake flour for a gluten-free blend can also work, just be cautious to adjust other liquid ingredients accordingly. Enjoy with peace of mind!
Can I use a different frosting instead of cinnamon cream cheese frosting?
The more the merrier! Try a simple vanilla buttercream or even a caramel frosting if you want something sweeter. Feel free to get creative by infusing your frosting with pumpkin spice or even chocolate for a decadent twist!

Irresistible Apple Pie Cupcakes with Creamy Cinnamon Frosting
Ingredients
Equipment
Method
- In a medium saucepan over medium heat, combine the finely diced tart apples, brown sugar, cornstarch, ground cinnamon, and water. Cook for about 10–12 minutes, stirring occasionally, until the apples are tender and most of the liquid has evaporated. Once done, remove from heat and allow the apple compote to cool completely before using it to fill your Apple Pie Cupcakes.
- Preheat your oven to 350°F (175°C), ensuring it's properly heated for even baking. Meanwhile, line a cupcake pan with cupcake liners to prevent sticking and make cleanup easier.
- In a large mixing bowl, whisk together the cake flour, baking powder, additional ground cinnamon, and salt until evenly combined. Set the bowl aside while you work on the wet ingredients.
- In another bowl, cream the softened unsalted butter until light and fluffy, about 2-3 minutes. Gradually add the granulated sugar, continuing to beat for an additional 2 minutes. Incorporate the eggs, one at a time, mixing well after each addition, and then stir in the vanilla extract.
- Gently fold the dry ingredients into the wet mixture, alternating with the milk. Mix just until everything is combined and smooth.
- Using a scoop or spoon, fill each cupcake liner about two-thirds full with batter.
- Place the filled cupcake pan in the preheated oven and bake for 18–20 minutes, or until a toothpick inserted into the center comes out clean. Allow the cupcakes to cool in the pan for 5 minutes before transferring them to a wire rack to cool completely.
- In a mixing bowl, beat the softened cream cheese and remaining butter until smooth and creamy. Gradually add the powdered sugar, cinnamon, and vanilla extract, mixing until well combined.
- Once the cupcakes are completely cooled, fill the center with the cooled apple compote, then generously pipe the frosting on top.
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