Apple Pie Cupcakes

These soft, fluffy apple pie cupcakes are stuffed with a homemade apple compote that tastes just like classic pie filling and topped with a cinnamon cream cheese frosting. They’re such a cozy treat for chilly days. I love making them when apples are everywhere at the market—it just feels like autumn in the kitchen.

A Little Baker’s Note

I’ll be honest—I think these are one of the cutest bakes I’ve done lately. The frosting lattice on top looks just like tiny pies. It’s the kind of dessert that gets a little “wow” when you bring them to the table, even if people pretend they’re too old to be charmed by cupcakes.

The apple compote in the middle really seals the deal. It’s like having a hidden apple pie tucked inside a soft, spiced cupcake. Perfect for anyone who loves the flavor of pie but doesn’t want to fuss with pastry. And if you do love making pies, this is a fun twist to add to your fall baking list.

Why You’ll Want to Bake These

• Tender, spiced cupcakes: They’re wonderfully soft, with just enough cinnamon to feel warm and seasonal. I always find that cupcakes are less intimidating than big cakes, so this is a nice project for a cozy afternoon.
• Homemade apple filling: This isn’t just chopped apple thrown in—it’s a cooked compote that tastes like real pie filling. It makes the cupcakes so moist and flavorful.
• Cinnamon cream cheese frosting: Rich, smooth, and spiced just right. The cream cheese balances the sweetness beautifully, so it never feels too heavy.
• Charming design: The frosting “lattice” on top makes them look like mini pies. When I made them for a fall gathering, they were the first thing people grabbed.

Helpful Tools in My Kitchen

You don’t need fancy bakery equipment, but a few things make life easier:

• Hand mixer: I use mine all the time for creaming butter and sugar. You can do it by hand if you’re patient, but a mixer saves your arm.
• 12-hole muffin pan: Nothing fancy here—just your standard muffin tin.
• Cupcake liners: I like to use brown parchment liners for a rustic look. Sometimes I go with fun seasonal prints for parties.
• Piping bag and tips: A piping bag makes it easy to get those lattice lines. If you don’t have one, you can always use a zip-top bag with the corner snipped. For the lattice, I like a ribbon or basketweave tip, but any flat tip works. For the border, I use an open star tip—it’s easy to find and gives a pretty finish.

A Word on Ingredients

Let’s talk ingredients the way I would with a friend over coffee.

• Apples: Go for tart apples that hold their shape—like Honeycrisp or Granny Smith. They balance the sweetness nicely. I always peel and dice them finely so they cook evenly.
• Brown sugar and cornstarch: Brown sugar gives that classic caramel-like sweetness. Cornstarch thickens the compote so it’s not watery in the cupcakes.
• Ground cinnamon: Don’t skimp—it’s what gives the filling and frosting that cozy, spiced aroma.
• Water: Adjust as you go. I often add splashes as the apples cook if things get too dry. Don’t be afraid to keep an eye on it.
• Cake flour: This makes the cupcakes lighter and more tender. If you don’t have it, you can make a substitute with all-purpose flour and cornstarch.
• Unsalted butter: Let it soften on the counter so it creams properly with sugar. Cold butter will leave lumps.
• Eggs: Room temperature eggs blend in better, giving you a smoother batter.
• Vanilla extract: I love using real vanilla for depth of flavor.
• Milk: I often use oat or almond milk since that’s what I keep around. Any milk works fine.
• Cream cheese: Bring it to room temperature for frosting. Cold cream cheese will stay lumpy, no matter how long you beat it.
• Powdered sugar: For that smooth, sweet frosting base.

Let’s Bake These Apple Pie Cupcakes

1. Make the Apple Filling

In a small pot, stir together your diced apples, brown sugar, cornstarch, cinnamon, and water. Cover and bring to a boil over medium-high heat. Once boiling, uncover and let it cook down, stirring often. You’re looking for tender apples with a thick, jammy texture. If it gets too dry, add a splash more water. Don’t wander too far—apple compote can scorch if you forget about it. Once done, transfer to a bowl and let it cool.

Tip from my kitchen: I sometimes make the filling a day ahead. It thickens even more in the fridge, and it’s one less step on baking day.

2. Make the Cupcakes

• Preheat your oven to 350°F. Line your muffin pan with cupcake liners.
• In a bowl, whisk together flour, baking powder, cinnamon, and salt.
• In another large bowl, beat softened butter with a hand mixer until creamy. Add sugar and beat until light and fluffy. Add eggs one at a time, mixing well between each. Stir in vanilla extract.
• Sift in half the dry ingredients and mix on low until barely combined. Pour in half the milk and mix briefly. Repeat with remaining dry ingredients and milk, mixing just until smooth.
• Fill the liners about two-thirds full. Bake for around 20 minutes. I always test with a toothpick—if it comes out clean, they’re done. Let them cool in the pan for 5–10 minutes before moving them to a wire rack.

3. Make the Frosting

• In a bowl, beat softened butter until creamy. Add cream cheese, powdered sugar, cinnamon, and vanilla. Beat on low speed until it’s thick, smooth, and spreadable. Don’t rush this part—a few extra seconds makes all the difference for silky frosting.

Personal note: I sometimes make extra frosting for those who like a heavy swirl. It keeps in the fridge for a few days.

4. Assemble the Cupcakes

• Use a small melon baller or paring knife to carve a little well in the center of each cooled cupcake.
• Spoon in cooled apple compote. Add a little more on top if you want them extra loaded.
• Fill a piping bag with the cinnamon cream cheese frosting. Pipe two crisscrossing lines over the top to mimic pie lattice. Switch tips if you like and pipe a border around the edge. It’s such a fun, bakery-style finish, but don’t worry if it’s not perfect—homemade charm is half the joy.

Keeping Them Fresh

Store these cupcakes in an airtight container in the fridge for up to 3 days. I always let them sit at room temperature for 20–30 minutes before serving so the frosting softens back up.

If you want to save some for later, you can freeze them (in a container) for about a month. Just thaw overnight in the fridge or for a few hours on the counter. I’ve done this before to have a batch ready for surprise visitors.

More Apple Treats for Cozy Days

If you’re like me and love baking with apples, don’t stop here. Try making little apple hand pies for a rustic treat, or a classic apple crisp with a big scoop of vanilla ice cream on top. They’re my go-tos for fall gatherings, and there’s just something so comforting about the smell of apples and cinnamon filling the house.

I hope you’ll try these apple pie cupcakes soon. They’re the kind of bake that feels like sharing a little bit of autumn with the people you love. Let me know how they turn out for you—I’d love to hear about your kitchen adventures.

Try other Cupcake recipes:

• Vanilla Buttercream Frosting
• Small Batch Vanilla Cupcakes
• Raspberry Cupcakes