Name: Apple Cheesecake Mini 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· 4.7 from 33 reviews

If you’re anything like me, you love the cozy flavors of fall desserts, but sometimes the idea of making a big cake can feel overwhelming. That’s exactly why I adore this Apple Cheesecake Mini Cupcakes Recipe. These bite-sized delights combine the tart sweetness of apples, creamy cheesecake, and a crunchy crumb topping all in one perfect little package. They’re not just easy to make but absolutely fan-freaking-tastic at any gathering or as a special treat after dinner. Trust me, once you try these, you’ll want to make them again and again.

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Why This Recipe Works

Perfect Balance of Flavors: The tart apples paired with smooth, sweet cheesecake and a cinnamon-oat crumb topping create layers of irresistible taste.
Mini Size Convenience: These cupcakes are portable and portion-controlled, making them great for parties or quick snacks without the hassle of slicing cake.
Simple to Assemble: No complicated techniques here—just straightforward mixing and layering that you’ll enjoy doing.
Versatile Serving Options: Enjoy them right out of the fridge or warmed up with a drizzle of caramel sauce for an extra indulgent touch.

Apple Cheesecake Mini Cupcakes, fall dessert recipes, easy mini cupcake recipes, apple desserts, cheesecake cupcake recipes - 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

The ingredients in this Apple Cheesecake Mini Cupcakes Recipe come together to give you that classic apple crisp feel but in a fun cheesecake cupcake form. I recommend picking apples that are firm and tart like Granny Smith or Honeycrisp for the best contrast with the creamy filling. Also, make sure your cream cheese is softened to room temperature for smooth mixing.

Apple Cheesecake Mini Cupcakes, fall dessert recipes, easy mini cupcake recipes, apple desserts, cheesecake cupcake recipes - Flat lay of a small pile of golden graham cracker crumbs, a neat mound of light brown sugar, a sprinkle of ground cinnamon in a small white bowl, a few curls of melted unsalted butter in a white ceramic dish, a small bowl of all-purpose flour, a heap of quick-cooking oats, a white ceramic bowl with a dusting of ground nutmeg, two medium-small peeled apples chopped finely, a small white ceramic bowl with freshly squeezed lemon juice, a block of soft cream cheese on a plain white plate, a clean whole brown egg, a small white bowl with granulated sugar, a small white bowl of vanilla extract, a small white bowl of cornstarch, and a white ceramic dish with golden caramel sauce placed on a clean white marble surface, soft natural light, photo taken with an iPhone, professional food photography style, fresh ingredients, white ceramic bowls, no bottles, no duplicates, no utensils, no packaging --ar 2:3 --v 7 --p m7354615311229779997

Graham cracker crumbs: They form the buttery crunchy base that holds everything together.
Sugar & cinnamon: Both appear in several layers for that warm, cozy sweetness and spice.
Unsalted butter: Melted butter binds the crust and crumb topping perfectly without overpowering flavors.
All-purpose flour: Helps thicken the crumb topping and cheesecake filling to the right consistency.
Quick-cooking oats: Adds a bit of texture and rustic charm to the topping.
Nutmeg: This subtle spice elevates the apple and cinnamon combo without stealing the show.
Apples: The star of the show—peeling and finely chopping them allows even distribution and bites full of fresh flavor.
Lemon juice: Keeps the apples bright and prevents browning.
Cornstarch: Ensures your apples stay juicy but not soggy by thickening their natural juices.
Cream cheese: Look for full-fat softened cream cheese for the dreamiest texture and richest taste.
Egg: Binds the cheesecake filling without making it rubbery.
Vanilla extract: Adds a sweet floral note that complements the apples and cinnamon.
Caramel sauce: Optional but highly recommended for drizzling—it brings that extra wow factor.

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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 of the best parts about this Apple Cheesecake Mini Cupcakes Recipe is how easy it is to personalize. Over the years, I’ve played with the toppings and spices, and honestly, it’s fun to experiment with what suits your family or guests.

Variation: I once swapped out the cinnamon for pumpkin pie spice during the holidays, and the warm fall vibes were instant—a great twist if you love that seasonal chai flavor combo.
Dietary modification: If you want to make it gluten-free, try almond flour or gluten-free oat flour for the crust and crumb topping—I’ve had success without losing texture.
Fruit swap: Pears or even peaches work nicely if you want to switch things up beyond apples.

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

Step 1: Prep and Chill the Crust

Start by lining your cupcake pan with paper liners. Then mix your graham cracker crumbs, sugar, and cinnamon in a bowl. Add melted butter and stir until everything is well-coated—the mixture should look like wet sand. Press about 2 tablespoons into the bottom of each liner, creating a firm base. I like to pop the pan in the fridge for at least 10 minutes here; it helps the crust hold up when the wet cheesecake filling goes on top.

Step 2: Make the Crumb Topping

Combine flour, brown sugar, oats, cinnamon, and nutmeg in a bowl. Stir in melted butter until the mixture forms coarse crumbs. Set this mixture aside in the fridge while you move on to the cheesecake filling—keeping it chilled helps the topping crisp up nicely when baked.

Step 3: Whip Up the Cheesecake Filling

In a large bowl, beat the softened cream cheese with sugar, vanilla, and flour until smooth—scrape the bowl edges so no lumps remain. Add the egg and mix just until combined; overmixing can cause cracks later, so keep it gentle. Spoon the filling evenly over each crust, filling each cup about two-thirds full.

Step 4: Prep and Add the Apple Filling

Toss the finely chopped apples with lemon juice to prevent browning, then stir in brown sugar, cornstarch, cinnamon, and nutmeg. This mixture thickens during baking and adds juicy pockets of apple flavor. Spoon the apple mixture on top of the cheesecake layer. Don’t be shy—fill close to the top and gently press the apples down with your hand so everything fits snugly.

Step 5: Top and Bake

Sprinkle a generous amount of the cinnamon oat crumb topping over each cupcake. This crumb layer becomes beautifully golden and crunchy in the oven. Bake at 325°F for about 28-30 minutes until the edges are set and the tops are lightly golden. Once baked, allow them to cool in the pan for 30 minutes before carefully lifting them out to chill in the fridge.

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Pro Tips for Making Apple Cheesecake Mini Cupcakes Recipe

Softened Cream Cheese is Key: Make sure your cream cheese is fully softened to avoid lumps and get an ultra-smooth filling.
Don’t Overmix the Batter: When adding the egg, mix gently to prevent cracking during baking.
Chill the Crust and Topping: Cooling these parts before assembly helps the textures hold up beautifully in the oven.
Use Fresh Apples: Always peel and finely chop apples—they bake better and fit perfectly in these mini cupcakes.

How to Serve Apple Cheesecake Mini Cupcakes Recipe

Apple Cheesecake Mini Cupcakes, fall dessert recipes, easy mini cupcake recipes, apple desserts, cheesecake cupcake recipes - This image shows a stack of three mini cheesecakes with a crumbly texture. Each cheesecake has four layers: the bottom layer is a golden brown crumbly base, followed by a smooth, light yellow cheesecake layer. Above that is a chunky layer of diced apples mixed with a brown sauce, and the top layer is a thick crumbly streusel topping with bits of nuts. The cheesecakes are sitting on a white marbled surface with a green blurred background. Photo taken with an iphone --ar 2:3 --v 7

Garnishes

I love adding a drizzle of warm caramel sauce just before serving—it adds that silky sweetness that pairs perfectly with the tart apples and creamy cheesecake. Sometimes I sprinkle a tiny pinch of flaky sea salt on top of the caramel drizzle, which creates this irresistible sweet-and-salty combo. If you’re feeling fancy, a small dollop of whipped cream adds a dreamy finish.

Side Dishes

These mini cupcakes are perfect on their own since they’re so rich, but I like pairing them with a cup of hot apple cider or chai tea for a complete autumn vibe. For a brunch setting, they’re delightful alongside a sharp cheddar cheese board or spiced nuts.

Creative Ways to Present

For holiday parties, I like arranging them on a wooden tray with sprigs of fresh rosemary and tiny cinnamon sticks around for a rustic look. You can also serve them in cute mini cupcake stands or even wrapped individually in clear cellophane tied with twine for easy gifting.

Make Ahead and Storage

Storing Leftovers

After cooling, I store the Apple Cheesecake Mini Cupcakes in an airtight container in the fridge. They stay fresh and moist for up to 4 days, which is great if you want to prep ahead of time. Just keep the caramel sauce separate until you’re ready to serve.

Freezing

If I want to make a batch ahead, I freeze these mini cupcakes without the crumb topping (to keep it from getting soggy). I wrap them individually in plastic wrap and place them in a freezer-safe container for up to 3 months. When ready, I thaw overnight in the fridge and add a fresh sprinkle of the crumb topping or homemade crumble before serving.

Reheating

Reheating these is easy—pop a cupcake in the microwave for about 15 seconds or warm gently in a low oven (around 300°F) for 5-7 minutes. This softly melts the caramel and enhances the apple aroma without drying out the cheesecake.

FAQs

Can I use other types of apples in this Apple Cheesecake Mini Cupcakes Recipe?

Absolutely! While tart apples like Granny Smith or Honeycrisp work best to balance the sweetness, you can experiment with Fuji or Gala. Just keep in mind softer apples might become mushy faster, so chop them finely and watch your baking time.
Do I have to use paper liners for this recipe?

Paper liners make cleanup easier and keep the cupcakes intact when you remove them, but you can also grease the pan well and bake without liners if you prefer. Just be gentle when removing.
Can I make these cupcakes ahead of time?

Yes! In fact, making them a day ahead lets the flavors meld beautifully. Store them covered in the fridge and add any caramel drizzle or crumb topping just before serving.
Is there a way to make this recipe dairy-free?

You can try using dairy-free cream cheese and vegan butter alternatives; however, texture and taste might vary slightly. I recommend testing a small batch first if you’re not familiar with these substitutes.

Final Thoughts

This Apple Cheesecake Mini Cupcakes Recipe is truly one of those treats that feels special but never intimidating to make—I think that’s why it’s become a favorite in my kitchen and with friends. They capture all the best parts of apple crisp and cheesecake in a way that’s perfectly portable and shareable. Give this recipe a try, and I bet you’ll be coming back to it whenever you want that warm, comforting dessert that feels like a hug in cupcake form. Happy baking!