If you love the cozy flavors of apple crisp and the creamy richness of cheesecake, then you are going to absolutely fall in love with this Apple Crisp Cheesecake Muffins Recipe. These delightful treats perfectly combine a buttery graham cracker crust, smooth cheesecake batter, tart and juicy apples, and a crunchy cinnamon oat topping into one irresistible muffin-sized package. Whether you’re gearing up for a holiday gathering, brunch with friends, or just want the ultimate sweet snack, this recipe brings all the warm autumn vibes in every bite.

Ingredients You’ll Need
Gathering simple, wholesome ingredients is the first step to creating these melt-in-your-mouth Apple Crisp Cheesecake Muffins. Each one plays a vital role in building the layers of flavor, texture, and color that make this recipe so special.
- Graham cracker crumbs: Provide a crunchy and buttery base that brings classic flavor and a perfect crust texture.
- Granulated sugar (1/4 cup): Sweetens the crust just enough to balance the tartness of the apples.
- Unsalted butter (1/2 cup melted): Adds richness and helps bind the crust ingredients together beautifully.
- Cream cheese (16 ounces softened): The star of the cheesecake layer, giving it that smooth, creamy consistency.
- Granulated sugar (1/2 cup): Sweetens the cheesecake filling without overpowering it.
- Large eggs (2): Provide structure and help create a rich, silky texture.
- Vanilla extract (1 teaspoon): Brings a warm, sweet aroma to the filling.
- Apples (2 large, peeled, cored, and chopped): Fresh, juicy apples tossed in lemon juice for brightness and tart contrast.
- Lemon juice (1 tablespoon): Prevents the apples from browning and adds a hint of zing.
- All-purpose flour (1/4 cup): Essential for binding the crumb topping together.
- Brown sugar (1/4 cup packed): Adds a deep molasses sweetness to the crisp topping.
- Ground cinnamon (1/2 teaspoon): Infuses the entire muffin with classic spice warmth.
- Cold unsalted butter (1/4 cup cubed): Creates the tender, crumbly texture of the topping when cut in.
- Old-fashioned rolled oats (1/3 cup): Adds an irresistible chew and rustic crunch to the crisp topping.
How to Make Apple Crisp Cheesecake Muffins Recipe
Step 1: Prepare Your Workspace and Oven
Preheat your oven to 350°F (175°C) to get it ready to perfectly bake these muffins. Line a 12-cup muffin tin with paper liners to make sure your muffins come out effortlessly and keep their shape nicely.
Step 2: Make the Graham Cracker Crust
In a medium bowl, combine the crushed graham cracker crumbs and 1/4 cup of granulated sugar, then stir in the melted butter until everything is evenly moistened. This mixture will form a deliciously crunchy, buttery base for each muffin.
Step 3: Press the Crust Into Muffin Cups
Firmly press about a heaping tablespoon of the graham cracker mixture into the bottom of each muffin liner. This step ensures a sturdy foundation that won’t crumble when you bite into these dreamy cheesecake muffins.
Step 4: Whip the Cream Cheese Filling
In a large bowl, beat the softened cream cheese with 1/2 cup of granulated sugar until smooth and creamy. This is the luscious cheesecake element that will make these muffins utterly irresistible.
Step 5: Add Eggs and Vanilla
Beat the eggs in, one at a time, mixing well after each to incorporate air and create a velvety texture. Then, stir in the vanilla extract to deepen the flavor profile with warm sweetness.
Step 6: Fill Muffin Cups With Cheesecake Batter
Distribute the creamy cheesecake filling evenly over the graham cracker crusts in your muffin tin. This layer will bake into a rich, smooth surprise inside each muffin.
Step 7: Toss Apples With Lemon Juice
Toss the chopped apples with lemon juice in a bowl to keep them looking fresh and to add a little tang that balances the overall sweetness.
Step 8: Prepare the Crumble Topping
In another bowl, stir together the flour, brown sugar, and cinnamon. Cut in the cold cubed butter with a pastry blender or two forks until the mixture resembles coarse crumbs. Stir in the oats for classic apple crisp texture.
Step 9: Layer Apples Over Cheesecake
Spoon the lemon-coated apples over the cheesecake batter in each muffin cup. This adds the juicy, fruity layer that brings the apple crisp charm to the muffins.
Step 10: Add the Crunchy Crumble
Finish by sprinkling the crumb topping generously over the apple layer in every muffin cup. This crunchy topping bakes up golden and perfectly crisp.
Step 11: Bake to Perfection
Bake for 25-30 minutes in the preheated oven until the cheesecake filling has set. The muffins should have a lovely golden top and a fragrant apple-cinnamon aroma filling your kitchen.
Step 12: Chill Before Serving
Let the muffins cool completely in the pan, then transfer them to the refrigerator to chill for at least 2 hours. This resting time allows the cheesecake to firm up and makes each muffin easier to enjoy.
How to Serve Apple Crisp Cheesecake Muffins Recipe

Garnishes
These muffins shine on their own, but a light dusting of powdered sugar or a drizzle of caramel sauce can elevate their presentation and flavor. A small dollop of whipped cream or a sprinkle of chopped nuts adds delightful texture and visual appeal.
Side Dishes
Serve your Apple Crisp Cheesecake Muffins alongside a warm cup of spiced tea or freshly brewed coffee for a cozy treat. A scoop of vanilla ice cream or a fruit compote also complements the rich, creamy flavors beautifully for a more indulgent dessert.
Creative Ways to Present
For a fun brunch or party idea, arrange these muffins on a wooden serving tray surrounded by fresh apple slices and cinnamon sticks. You can also place them in decorative paper cups or gift boxes for giveaways or festive occasions.
Make Ahead and Storage
Storing Leftovers
Keep your Apple Crisp Cheesecake Muffins in an airtight container in the refrigerator. They will stay fresh and delicious for up to 4 days, making them perfect for a quick grab-and-go breakfast or snack.
Freezing
If you want to enjoy these muffins later, freeze them wrapped individually in plastic wrap and stored in a freezer-safe bag. They freeze beautifully and can be kept for up to 2 months without losing flavor or texture.
Reheating
To warm frozen or refrigerated muffins, microwave for 20-30 seconds or warm them in an oven set to 300°F (150°C) for 10-15 minutes. This brings back their just-baked softness and melts the crisp topping delightfully.
FAQs
Can I use a different type of apple for this recipe?
Absolutely! Granny Smith apples are great for tartness, but you can use Fuji, Honeycrisp, or Gala for a sweeter apple flavor. Just be sure to adjust sugar levels based on the apple’s sweetness.
Do I need to use paper liners in the muffin tin?
While paper liners make clean-up easier and muffin removal simpler, you can also grease the tin well and bake without liners if you prefer a crisper exterior edge on your muffins.
Can I make this recipe dairy-free?
For a dairy-free version, try using dairy-free cream cheese and butter substitutes. The texture might be slightly different but still delicious and creamy.
What if I don’t have rolled oats for the topping?
If you don’t have rolled oats, you can substitute quick oats or even chopped nuts to add that lovely crunch in your crumble topping.
Can these muffins be made mini or jumbo size?
Yes! Just adjust the baking time accordingly. Mini muffins will need less time (around 15-20 minutes), while jumbo muffins will take longer (35-40 minutes). Keep an eye on the cheesecake layer to make sure it sets properly.
Final Thoughts
There is truly something magical about these Apple Crisp Cheesecake Muffins Recipe that makes them a must-bake for anyone who loves comforting, homey desserts with multiple layers of flavor and texture. Whether you’re sharing with family or treating yourself, these muffins bring warmth and joy in every bite. Give this recipe a try—you won’t regret it!
Print
Apple Crisp Cheesecake Muffins Recipe
- Prep Time: 0h 20m
- Cook Time: 0h 30m
- Total Time: 2h 50m
- Yield: 12 individual cheesecakes
- Category: Dessert
- Method: Baking
- Cuisine: American
- Diet: Vegetarian
Description
These Apple Crisp Cheesecakes are a delightful fusion of creamy cheesecake and warm apple crisp, baked in individual muffin cups for a perfect single-serving treat. A crunchy graham cracker crust forms the base, topped with smooth cheesecake batter, a layer of cinnamon-spiced apples, and a crumbly oat topping, making them an irresistible dessert for any occasion.
Ingredients
Crust
- 24 graham cracker squares (about 12 full sheets), crushed into crumbs
- 1/4 cup granulated sugar
- 1/2 cup unsalted butter, melted
Cheesecake Filling
- 16 ounces cream cheese, softened
- 1/2 cup granulated sugar
- 2 large eggs
- 1 teaspoon vanilla extract
Apple Topping
- 2 large apples, peeled, cored, and chopped
- 1 tablespoon lemon juice
Crumble Topping
- 1/4 cup all-purpose flour
- 1/4 cup packed brown sugar
- 1/2 teaspoon ground cinnamon
- 1/4 cup cold unsalted butter, cubed
- 1/3 cup old-fashioned rolled oats
Instructions
- Preheat Oven and Prepare Pan: Preheat your oven to 350°F (175°C) and line a 12-cup muffin tin with paper liners to prevent sticking and make serving easy.
- Make Graham Cracker Crust: In a medium bowl, combine the crushed graham cracker crumbs with 1/4 cup granulated sugar. Stir in the melted butter until the mixture is evenly moistened.
- Form Crusts: Press a heaping tablespoon of the graham cracker mixture firmly into the bottom of each muffin cup to create the crust layer.
- Prepare Cheesecake Batter: In a large bowl, beat the softened cream cheese and 1/2 cup granulated sugar together until smooth and creamy, ensuring no lumps remain.
- Add Eggs and Flavoring: Incorporate the eggs one at a time into the cream cheese mixture, mixing well after each addition, then blend in the vanilla extract to enhance flavor.
- Fill Muffin Cups: Evenly distribute the cheesecake batter over the graham cracker crusts in each muffin cup using a spoon or small spatula.
- Toss Apples: In a separate bowl, toss the chopped apples with lemon juice to prevent browning and add a subtle tartness.
- Prepare Crumble Topping: Combine the flour, brown sugar, and cinnamon in another bowl. Use a pastry blender or two forks to cut in the cold cubed butter until the mixture becomes crumbly. Stir in the old-fashioned rolled oats to complete the topping.
- Add Apples to Cheesecake: Spoon the lemon-coated chopped apples evenly over the cheesecake batter in each muffin cup.
- Top with Crumble: Generously sprinkle the prepared crumble topping over the apples in each cup to create a crispy finish.
- Bake: Bake the cheesecakes in the preheated oven for 25-30 minutes, or until the cheesecake filling is set and lightly golden on top.
- Cool and Chill: Allow the cheesecakes to cool completely in the muffin tin to firm up, then transfer them to the refrigerator. Chill for at least 2 hours before serving to let flavors meld and texture set.
Notes
- Make sure the cream cheese is softened to room temperature for a smooth batter without lumps.
- Use tart apples like Granny Smith for a balanced sweetness with the crumble topping.
- Chilling the cheesecakes is crucial for proper texture and easier removal from the liners.
- Store leftover cheesecakes covered in the refrigerator for up to 3 days.
- You can add chopped nuts like pecans to the crumble for added crunch if desired.

