Mini Apple Crisp Cheesecakes (Easy Fall Dessert Recipe)

Fall baking is one of my absolute favorite things to do. As soon as the leaves start to change, my kitchen fills with the smell of cinnamon, nutmeg, and apples. My husband James always teases that I could open a bakery this time of year because there’s always something cooling on the counter. Ariya, my 5-year-old little girl, is the first one to peek her head into the kitchen and see what I’m baking this time, while Cameron, my 13-month-old, just points at everything and says “more.” These little Mini Apple Crisp Cheesecakes are the kind of treat my family gets excited about—the perfect blend of creamy cheesecake, warm cinnamon apples, and a crunchy crisp topping all packed into a handheld dessert.

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What Is This Recipe Exactly?

Mini Apple Crisp Cheesecakes combine three classic desserts into one irresistible bite: creamy New York-style cheesecake, gooey apple pie filling, and buttery crisp topping. They’re baked in muffin tins instead of a springform pan, making them simple, approachable, and perfect for serving at holidays, bake sales, or just cozy fall nights at home.

Why This Recipe Works

This recipe works because it layers complementary flavors and textures. The graham cracker crust creates a sturdy, buttery base. The cheesecake filling is smooth, tangy, and lightly sweet, which balances the spiced apple topping. The apple layer adds warmth, natural sweetness, and that fall flavor everyone craves. Finally, the crisp topping provides crunch and buttery richness. Together, every bite hits all the notes—sweet, creamy, spiced, and crunchy—without being overly heavy.

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Ingredient Breakdown: What They Do

• Graham Crackers, Sugar, Cinnamon, Butter (Crust): The base layer adds stability and a nutty, spiced flavor that complements the apples.
• Cream Cheese, Sugar, Cinnamon, Vanilla, Eggs (Cheesecake): Cream cheese provides the tangy, creamy body; sugar balances; cinnamon and vanilla enhance flavor; eggs give structure.
• Apples, Lemon Juice, Spices, Brown Sugar, Cornstarch (Apple Filling): Apples provide natural sweetness; lemon juice prevents browning; spices add depth; cornstarch thickens.
• Flour, Oats, Brown Sugar, Cinnamon, Butter (Crumble): Creates the signature crisp topping with crunch and warmth.

When to Serve / Serving Ideas

These are perfect for:

• Thanksgiving and holiday dessert tables when you want an alternative to traditional pie.
• Bake sales and potlucks—individually portioned desserts are always a hit.
• Fall family gatherings when apples are in season.
• Weeknight treats because they can be made ahead and enjoyed over several days.

Serve them with a drizzle of caramel sauce, a dollop of whipped cream, or even a scoop of vanilla ice cream for an extra indulgent dessert.

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Make Ahead & Storage Tips

These cheesecakes are great make-ahead desserts. You can bake them up to two days in advance and store them in the refrigerator. Keep them in an airtight container for freshness. They also freeze beautifully—just skip the caramel drizzle until serving. To freeze, wrap tightly in plastic wrap and store in a freezer bag for up to 2 months.

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Why You’ll Love This Recipe

• Easy to make in a muffin tin—no springform pan or water bath needed.
• Combines the best of cheesecake, apple pie, and apple crisp.
• Perfectly portable for sharing.
• Simple ingredients with big flavor payoff.
• Great for both beginner bakers and seasoned cooks.

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FAQ – Mini Apple Crisp Cheesecakes

Can I use apple pie filling instead of fresh apples?
Yes, canned apple pie filling can be used for convenience. However, I recommend chopping the filling into smaller pieces so it sits nicely on top of the cheesecakes. Fresh apples give you better texture and control over the sweetness and spice, but pie filling is a great shortcut if you’re pressed for time.

What apples are best for this recipe?
Granny Smith apples are the top choice because they’re tart and hold their shape when baked. Honeycrisp, Pink Lady, or Fuji also work if you prefer a sweeter filling. Avoid very soft apples like Red Delicious, which tend to turn mushy during baking.

How do I keep the crust from getting soggy?
The graham cracker crust bakes quickly and firms up nicely before the filling goes in, which prevents sogginess. Be sure to pre-bake the crust until set before adding cheesecake batter. Also, make sure your apple filling isn’t overly wet—if your apples release too much liquid, sprinkle in an extra pinch of cornstarch.

Do I have to use a stand mixer for the cheesecake batter?
No, you can absolutely use a hand mixer. The key is to beat the cream cheese long enough to remove all lumps—about 4–5 minutes. Scrape the bowl often to ensure everything is smooth.

Can I double this recipe?
Yes, you can easily double it. This recipe makes 16 minis, but doubling will give you about 32. Use two muffin tins and rotate them halfway through baking for even results.

How do I know when the cheesecakes are done baking?
The centers should jiggle slightly when shaken but not be soupy. They’ll continue to set as they cool. Overbaking can cause cracks, but since these are topped with apples and crumble, small imperfections won’t show.

Can I make these gluten-free?
Yes. Use gluten-free graham crackers for the crust and substitute almond flour for the crumble topping. Ensure all other ingredients (like oats) are certified gluten-free.

Can I make these dairy-free?
You can try dairy-free cream cheese and butter substitutes. The texture may be slightly different, but the flavor will still be delicious. Full-fat plant-based cream cheeses work best.

Why did my cheesecake crack?
Overmixing eggs or overbaking often causes cracks. Mix eggs just until combined and pull cheesecakes out when they’re still a little jiggly. Don’t worry if they crack—your apple topping and crumble will cover them beautifully.

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Can I freeze these mini cheesecakes?
Yes! Cool completely, skip the caramel drizzle, then wrap tightly in plastic wrap. Freeze for up to 2 months. Thaw overnight in the fridge before serving.

What’s the best way to serve these at a party?
Serve chilled or at room temperature on a dessert platter. Drizzle caramel just before serving for presentation. Guests love that these are individual portions—no messy slicing required.

Can I use other fruits instead of apples?
Yes, pears, peaches, or even berries can work. Adjust sugar levels depending on the fruit’s sweetness, and keep the cornstarch to help thicken juices.

How long do these last in the fridge?
Stored properly in an airtight container, they last 3–4 days. After that, the crust may soften slightly.

Why are my cheesecakes sinking in the middle?
This can happen if the batter is overmixed or if the oven door was opened during baking. The good news is the apple topping and crumble cover any sinking, so they’ll still look (and taste) amazing.

Can I use cupcake liners?
Yes, and I recommend them for easy removal. If you don’t have liners, lightly grease the muffin pan, but liners give the cleanest look.

Can I add nuts to the topping?
Yes, chopped pecans or walnuts mix beautifully into the crumble topping for extra crunch.

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Variations & Substitutions

• Fruit swap: Try pears or peaches.
• Nut topping: Add pecans or walnuts.
• Spice changes: Add cardamom or allspice for deeper flavor.
• Crust variation: Use gingersnap cookies instead of graham crackers for a spicier base.

Leftover Ideas

• Crumble chilled leftovers into a parfait with whipped cream.
• Chop into bite-sized squares for a dessert platter.
• Freeze leftovers to enjoy later in the season.

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Budget Breakdown

• Graham crackers: $2
• Cream cheese: $4
• Apples: $2
• Pantry staples (sugar, flour, oats, spices, butter): $5
• Total: ~$13 (16 servings = $0.81 per serving)

Perfect for Fall Baking and Thanksgiving Dessert

There’s something about apples, cinnamon, and cheesecake that just feels like fall in every bite. These Mini Apple Crisp Cheesecakes are the ultimate cozy dessert to make when the weather turns crisp and you’re craving those classic autumn flavors. The combination of spiced apples and buttery crumble topping makes them feel just as festive as a traditional apple pie, but in a fun, handheld form that’s easier to serve.

They’re also a fantastic choice for Thanksgiving dessert because they give guests another option beyond pumpkin or pecan pie. Sometimes people want a little variety, and having these minis on the dessert table adds that wow factor. They’re portioned perfectly so everyone can grab one without having to slice into a big cake or pie, which also makes them a great pick for potlucks or family gatherings where there are multiple desserts to sample.

Plus, they hold up beautifully if made ahead—so while you’re busy juggling turkey, side dishes, and all the holiday chaos, you can feel confident knowing dessert is ready to go. Top them with caramel drizzle or whipped cream just before serving, and you’ll have a treat that tastes like fall and looks like you went all out.

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Lighten-Up Version

• Use reduced-fat cream cheese.
• Cut sugar in half or use a sugar substitute.
• Swap butter for coconut oil in the crust and crumble.
• Skip caramel drizzle for fewer calories.

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Reader Favorite Tips and Ideas

• “Add pecans to the crumble for crunch!”
• “Drizzle caramel AND chocolate for extra indulgence.”
• “Freeze half to save for later.”

Troubleshooting Tips

• Crust too crumbly? Add more melted butter.
• Filling too runny? Make sure cream cheese is room temperature.
• Apples too watery? Add an extra pinch of cornstarch.

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A Crowd-Pleasing Dessert for Any Gathering

One of the reasons I love these Mini Apple Crisp Cheesecakes is how well they fit into just about any gathering. Whether it’s a cozy fall dinner with friends, a casual Sunday family get-together, or a big Thanksgiving spread, they’re the kind of dessert that feels both special and approachable. Everyone loves the familiar flavors of apple crisp and cheesecake, but presenting them in individual portions makes them even more exciting.

They also travel well, which means you can bring them to a potluck, school event, or holiday party without worrying about slicing a messy pie or carrying a whole cheesecake. Just pop the liners into a container and you’re good to go. And since they’re made in muffin tins, you can easily double or even triple the batch to feed a crowd.

If you’re anything like me, you know desserts at Thanksgiving or Christmas tend to compete for attention. With pumpkin pie, pecan pie, and maybe even a chocolate dessert on the table, it’s nice to have something bite-sized so guests can try a little of everything. These mini cheesecakes offer the perfect balance of creamy, spiced, and sweet, ensuring they’ll disappear quickly no matter where you serve them.

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Nutrition Information (per cheesecake, approx.)

• Calories: ~210
• Carbs: 24g
• Protein: 3g
• Fat: 11g
• Sugar: 14g
• Fiber: 2g

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My Personal Kitchen Notes

This recipe is one of my favorite fall desserts because it’s so forgiving. Even if the cheesecakes crack or the apple topping looks rustic, they always taste incredible. I find pre-chilling the crusts before baking makes them even sturdier. And if you have leftover apple topping, spoon it over oatmeal or ice cream—it’s delicious.

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My Final Thoughts

Mini Apple Crisp Cheesecakes are the kind of dessert that feels both special and comforting. They’re elegant enough for holidays yet simple enough for a weeknight treat. They combine the best of fall flavors in every single bite, and I promise your friends and family will love them as much as mine do.

Psst… Other Fall Must-Try Desserts

If your oven’s still warm and you’re craving more cozy bites, here are some stellar fall desserts you might want to try next:

• Deep Fried Apple Hand Pies – Think gooey spiced apples tucked in flaky pockets, fried until golden, and glazed while still warm. It’s like a fair in your kitchen.
• Apple Crumb Cheesecake Pie – If you can’t decide between apple pie or cheesecake, why not both? Creamy, crumbly, and all-around irresistible.
• No-Bake Pumpkin Cheesecake Bars – No oven? No problem. These bars marry velvety pumpkin-spiced cheesecake with a buttery crust—perfect for when you just wanna chill.
• Oven-Baked Bloomin’ Apples – These apple blooms burst open like fall flowers, then bake into tender caramel-drizzled goodness. Serve with ice cream, if you’re feeling indulgent.
• Apple Slab Pie – Because sometimes you need something big, rustic, and shareable. No details here—just go feast your eyes on that beauty.
• Pumpkin Roll – A spiced pumpkin sponge wrapped around a tangy cream cheese swirl. Looks fancy, bakes simply, hits all the holiday feels.

Mix, match, and layer these into your dessert repertoire—or just pick one and make it your new go-to with a mug of cider. Whatever you choose, fall just got a whole lot sweeter.