Name: Apple Cinnamon Cheesecake Cupcakes Recipe
Prep time: 20 min
Cook time: 30 min
Total time: 50 min
Cuisine: American
Ingredients: 3/4 cup graham cracker crumbs; 1 and 1/2 Tablespoons sugar; 1/2 teaspoon cinnamon; 3 Tablespoons unsalted butter, melted; 1/3 cup all-purpose flour; 1/3 cup light brown sugar; 1/3 cup quick-cooking oats; 3/4 teaspoon cinnamon; 1/8 teaspoon nutmeg; 2 and 1/2 Tablespoons unsalted butter, melted; 2 medium-small apples, peeled and chopped finely; 2 teaspoons freshly squeezed lemon juice; 1 and 1/2 teaspoons cinnamon; 1/4 teaspoon nutmeg; 2 Tablespoons light brown sugar; 1 and 1/2 teaspoons cornstarch; 10 oz cream cheese, softened; 6 Tablespoons sugar; 1 and 1/2 teaspoons vanilla extract; 2 teaspoons all-purpose flour; 1 egg; Caramel sauce

Jump to Recipe· 4.8 from 27 reviews

Hey there! If you’re craving a cozy dessert that perfectly balances creamy, fruity, and spiced flavors, then you’re going to adore this Apple Cinnamon Cheesecake Cupcakes Recipe. These little beauties are like a hug in cupcake form—soft cream cheese filling, tender apples bursting with cinnamon, and a crumbly topping that adds just the right amount of crunch. Trust me, once you try these, they’ll become your go-to for both casual family treats and fancy get-togethers.

💛

Why This Recipe Works

Layered Flavors: Each layer from crust to crumb topping brings a different texture and taste that complements the others beautifully.
Comforting Spice Blend: Cinnamon and nutmeg warm the apples perfectly without overwhelming the delicate cream cheese.
Mini Size, Big Impact: The cupcake format makes portioning easy and they’re perfect for sharing or impressing guests.
Simple Ingredients: You don’t need anything fancy—just pantry staples and fresh apples for a surprisingly stunning result.

Apple Cinnamon Cheesecake Cupcakes, apple cinnamon cupcakes, cheesecake cupcakes with apples, spiced apple dessert, easy apple cheesecake treats - The image shows a close-up of several small muffin cups filled with a diced apple mixture that looks soft and cooked, topped with a crumbly golden-brown streusel layer. Each muffin cup is lined with white paper and placed in a dark muffin tin, resting on a white marbled surface. The crumb topping looks crunchy and uneven, with some larger chunks scattered on top. The diced apples beneath are a warm light brown color with soft edges, giving a cozy baked look. Photo taken with an iphone --ar 2:3 --v 7

Ingredients & Why They Work

Let’s talk ingredients because understanding them helps you nail this Apple Cinnamon Cheesecake Cupcakes Recipe every single time. The graham cracker crust sets a buttery, spiced foundation, while the apples mix tanginess with warmth. The cream cheese filling is velvety and smooth, balancing everything out.

Graham cracker crumbs: Provide a crunchy, buttery base that’s lightly sweetened and spiced with cinnamon for extra warmth.
Sugar (granulated and brown): Brown sugar adds caramel notes while white sugar sweetens the cream cheese batter evenly.
Cinnamon and nutmeg: Essential spices that give the apples and crumbs that classic fall flavor everyone loves.
Unsalted butter: Melts into the crust and crumb topping for richness and moisture, making everything hold together perfectly.
Apples: I recommend medium-small, firm varieties like Honeycrisp or Granny Smith for their tartness and texture.
Lemon juice: Keeps the apples bright and prevents browning, which is key for vibrant flavor.
Cornstarch: Thickens the apple filling so it’s luscious but not runny.
Cream cheese: The star of the cheesecake filling—it should be softened for smooth mixing.
Vanilla extract: Adds a fragrant, cozy flavor that amplifies the cheesecake’s richness.
Egg: Binds the cheesecake filling so it holds its shape after baking.
All-purpose flour: Gives structure to both the cheesecake and crumb topping for balanced texture.

📝

Note: You’ll find the complete list of ingredients, along with their exact measurements, in the printable recipe card at the bottom of this post.

Tweak to Your Taste

One thing I love about this Apple Cinnamon Cheesecake Cupcakes Recipe is how easy it is to make your own. I’ve played around with extra seasonal twists that take these cupcakes over the top, and I encourage you to do the same!

Nutty Add-Ins: I sometimes sprinkle chopped pecans or walnuts on top before baking, adding a toasty crunch that pairs wonderfully with the cinnamon oats.
Spice it Up: Feel free to add a pinch of ground cloves or ginger to the apple filling for a bolder fall flavor.
Go Sugar-Free: Substitute the sugars with maple syrup or coconut sugar to keep it natural while preserving sweetness.
Make it Mini: This recipe works great with mini cupcake pans too—perfect for bite-sized party treats!

Step-by-Step: How I Make Apple Cinnamon Cheesecake Cupcakes Recipe

Step 1: Whip Up the Crust

Start by mixing your graham cracker crumbs with sugar and cinnamon. This combo really sets the cozy tone. Then stir in melted butter until it holds together when pressed. I use about 2 tablespoons of this mixture per cupcake liner, pressing firmly to create a sturdy base. Popping the crusts into the fridge while you prep the toppings keeps them firm so the layers stay neat!

Step 2: Prep the Crumb Topping

In a small bowl, mix flour, brown sugar, oats, cinnamon, and nutmeg, then stir in melted butter until coarse crumbs form. This crumb topping is the final crunchy layer that perfectly finishes each cupcake. Set it aside in the fridge to chill—it’s easier to sprinkle when cold.

Step 3: Make the Cheesecake Filling

Beat softened cream cheese with sugar, vanilla, and flour until silky smooth—this takes about 2-3 minutes. Then add the egg and mix just until combined; overmixing can add air bubbles and cracks. The batter should be creamy and luscious, ready to spoon over your chilled crusts.

Step 4: Prep the Apple Filling

Toss finely chopped apples with lemon juice, brown sugar, cornstarch, cinnamon, and nutmeg. These spices and the cornstarch help thicken the apples during baking while the lemon juice keeps them bright. Be sure the pieces are small—that way, each bite gets a perfect balance of apples and creamy cheesecake.

Step 5: Assemble and Bake

Spoon the cheesecake filling into each crust, filling about two-thirds of the paper cup. Then add your seasoned apples on top, pressing lightly to fit more in. Finally, sprinkle the chilled crumb topping generously—don’t be shy. Bake at 325°F for around 28-30 minutes until the cheesecake is set but still slightly jiggly in the center.

Step 6: Cool and Serve

Let the cupcakes cool in the pan for about 30 minutes before carefully removing them to chill in the fridge at least an hour. This helps them firm up and develop more flavor. When serving, I love drizzling warm caramel sauce over the top for that extra sweet finish—total game changer.

💡

Pro Tips for Making Apple Cinnamon Cheesecake Cupcakes Recipe

Softened Cream Cheese: Make sure your cream cheese is room temperature to avoid lumps and ensure a silky cheesecake filling.
Avoid Overbaking: The cupcakes are done when the edges are set but the center still jiggles slightly—this keeps them moist.
Chill Crust and Topping: Refrigerate the crust and crumb topping before baking for a crisp finish without sogginess.
Press Apples Gently: Don’t mash the apples when pressing them into the filling; gentle pressure keeps their texture intact.

How to Serve Apple Cinnamon Cheesecake Cupcakes Recipe

Garnishes

I usually stick to a simple caramel drizzle because it complements the cinnamon apples so well and adds that gorgeous sticky sweetness. Sometimes I’ll toss on some toasted chopped pecans for texture and a pop of nutty flavor. Fresh whipped cream is always welcome if you want an extra decadent touch!

Side Dishes

When I serve these cupcakes at brunch, I pair them with a light green salad with citrus vinaigrette or even a warm chai latte—both contrast the sweetness and spice beautifully. For dessert, they shine all on their own but also pair nicely with a scoop of vanilla ice cream.

Creative Ways to Present

For fall gatherings, I love placing these cupcakes inside little paper baskets with string-tied cinnamon sticks for a festive look. You can also serve them on beautiful wooden trays lined with parchment and dotted with fresh apple slices and mint leaves. It’s such a simple way to impress!

Make Ahead and Storage

Storing Leftovers

I keep leftover Apple Cinnamon Cheesecake Cupcakes tightly covered in an airtight container in the fridge for up to 4 days. The flavors actually meld over time, making them even tastier. Just be sure to bring them to room temperature or add a quick warm caramel drizzle before serving again.

Freezing

If you want to freeze them, wrap each cupcake individually in plastic wrap and place them in a freezer-safe container. They freeze beautifully for up to 2 months. When you’re ready, thaw overnight in the fridge and add fresh caramel sauce or whipped cream before eating.

Reheating

I find reheating in the microwave for about 15 seconds brings back just enough warmth without making the crumb topping soggy. If you want them a little warmer, 5 minutes in a low temp oven works too—just keep an eye on them so they don’t dry out.

FAQs

Can I make this Apple Cinnamon Cheesecake Cupcakes Recipe dairy-free?

Yes! Use dairy-free cream cheese alternatives and vegan butter for the crust and crumb topping. Keep in mind the texture might be slightly different, but the flavors will still shine through beautifully.
What kind of apples work best?

Medium-small apples like Honeycrisp, Granny Smith, or Fuji are ideal because they hold up well during baking and offer the right balance of tartness and sweetness. Avoid super soft varieties that turn mushy easily.
Can I prepare these cupcakes in advance?

Absolutely. You can assemble them a day ahead and keep them refrigerated, then bake right before serving for the freshest texture. Alternatively, fully baked cupcakes store well in the fridge and taste great after chilling.
Why do I need to chill the crust and topping before baking?

Chilling keeps the butter solidified, which helps the crust and topping stay crisp during baking and prevents them from blending too much into the wet fillings.
How do I avoid cracks in the cheesecake filling?

Don’t overmix the batter after adding the egg to avoid too much air. Bake at a low temperature and remove the cupcakes when they are slightly jiggly to prevent cracks as they cool.

Final Thoughts

This Apple Cinnamon Cheesecake Cupcakes Recipe holds a special place in my heart because it brings together all the best parts of fall desserts in the easiest, most delightful way. Whether you’re baking for a crowd or just wanting a sweet treat for yourself, these cupcakes deliver on flavor and comfort. I can’t wait for you to try them and maybe even put your own spin on the recipe. Let me know how they turn out—I’m rooting for your baking success!