Made with a buttery crumb crust, creamy base topped with a layer of crumb topping and apples, these mini cheesecakes with apple crumb topping are perfect for fall desserts.
Want to mix it up? Drizzle warm caramel sauce over each one of these mini cheesecakes for an extra indulgent bite.
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Recipe at a Glance
Prep: 25 min | Cook/Bake: 22 min | Chill Time: 2 hours
Main Ingredients: cream cheese, graham cracker crumb crust and a homemade apple crumb topping
Best For: fall desserts, parties, and make-ahead treats
Make Ahead: Needs about 2 hours of chilling and can be made a day in advance
Storage: Store covered in the refrigerator for up to 4 days
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Table of Contents
- Recipe at a Glance
- Tips for making Cheesecake "Cupcakes"
- Main Ingredients Needed
- Substitutions and Variations
- Step-by-Step Instructions
- Insider Tips from My Kitchen to Yours
- Storage & Serving Tips
- Recipe FAQ's
- More Recipes You'll Love!
- LOVE this recipe? SAVE it for Later!
- 🗒️Shopping List
- 📖 Recipe Card
- Food Safety Tips:
- 💬 Comments
Tips for making Cheesecake "Cupcakes"
- Lightly spray the paper liners with non-stick baking spray so the cheesecakes release cleanly when serving.
- Use a cookie scoop to portion the cheesecake batter evenly for uniform cupcakes.
- Allow the baked cheesecakes to cool completely, then chill for at least two hours so they set firmly and hold their shape.
Looking for more easy desserts with apples? Try my Apple Crumb Pie or my full size Cheesecake with Caramel Apple Crumb Topping.
Main Ingredients Needed
Below is a quick preview of the ingredients you’ll need. For exact amounts, check the recipe card below. You can also use the "Shopping List button" to create a printable shopping list, or the "Get Ingredients button" in the recipe card to order groceries online.
Substitutions and Variations
Crust Options: Replace the graham cracker crumbs with crushed vanilla wafers or gingersnap cookies for a different flavor.
Apple Choices: For this recipe I used HoneyCrisp, but you can choose your favorite!
Toppings: Add a drizzle of caramel sauce or a dollop of whipped cream just before serving for extra indulgence.
Spice Twist: Stir a pinch of nutmeg or allspice into the crumb topping for a deeper fall spice flavor.
This recipe has not been tested with other substitutions or variations. If you replace or add any ingredients, please let me know how it turned out in the comments below!
Step-by-Step Instructions
This section provides step-by-step photos and instructions to guide you through the recipe. For the complete printable version, scroll down to the recipe card below.
Step 1: Prepare the crust by mixing together the graham cracker crumbs, brown sugar, and melted butter. Press a heaping tablespoon into each cupcake liner.
Step 2: Make the cream cheese filling by beating the cream cheese until smooth, then mix in the sour cream, sugar, vanilla, and salt. Beat in the egg until just combined.
Step 3: Spoon about 2 tablespoons of filling over each crust.
Step 4: Prepare the apple layer by tossing the finely diced apples in lemon juice, brown sugar, and cinnamon.
Step 5: Evenly spoon the apple layer over the cheesecake layer.
Step 6: Make the crumb topping by combining the oats, flour, brown sugar, cinnamon, and salt. Cut the cold butter in using a fork or pastry blender until crumbly.
Step 7: Sprinkle the crumb topping over the apple layer.
Step 8: Bake the cheesecake cupcakes for 20-22 minutes until the centers are just set. Cool in the pan, then refrigerate for 2 hours.
Insider Tips from My Kitchen to Yours
✔️ DO spray the cupcake liners with non-stick baking spray so the mini cheesecakes release cleanly after chilling.
❌ DO NOT skip the chill time—without at least two hours in the fridge the cheesecakes won’t set properly and may fall apart when serving.
Storage & Serving Tips
Refrigerate: Store cooled mini cheesecakes in an airtight container for up to 5 days.
Freezer: Freeze fully cooled cheesecakes in a single layer until firm, then wrap individually and keep in an airtight container for up to 2 months.
Serving Tips: Serve chilled or let sit at room temperature for 10–15 minutes for the creamiest texture; top with caramel drizzle or whipped cream just before serving if desired.
Recipe FAQ's
To view the answers, simply click on the down arrow (⬇) next to each question. If you have any other questions not answered here, please leave a comment!
Yes, you can substitute Greek yogurt for the sour cream. Use the same amount of full-fat Greek yogurt for the best texture and richness. The cheesecakes will still be creamy, though the flavor may be slightly tangier.
Mini cheesecakes can crack or sink if they’re overbaked or if they cool too quickly. Bake just until the centers are set but still slightly jiggly—residual heat will finish the cooking. After baking, leave the cheesecakes in the turned-off oven with the door cracked for about 10 minutes before moving them to a cooling rack to let the temperature drop gradually and prevent sudden shrinkage.
More Recipes You'll Love!
Check out my other recipe for Cheesecake Cupcakes with Sour Cream Topping. Or you might like this recipe for Apple Cheesecake.
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🗒️Shopping List
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📖 Recipe Card
Mini Cheesecakes with Apple Crumb Topping
Video
Ingredients
- 1 cup graham cracker crumbs
- 3 tablespoons brown sugar
- 4 tablespoons melted butter
- 12 ounces cream cheese, softened
- ¼ cup sour cream
- ⅓ cup granulated sugar
- 1 large egg
- 1 teaspoon vanilla extract
- pinch of salt
- 1 ½ cups finely diced apples (Granny Smith or Honeycrisp work well)
- 1 tablespoon brown sugar
- ½ teaspoon cinnamon
- 1 teaspoon lemon juice
- ⅓ cup old fashioned oats
- ¼ cup brown sugar
- ¼ cup all purpose flour
- ½ teaspoon cinnamon
- pinch of salt
- 3 tablespoons cold butter, cut into cubes
Method
- Preheat oven to 325°F (160°C). Line a 12-cup muffin tin with paper liners and lightly spray with nonstick spray.
- Mix graham cracker crumbs, brown sugar, and melted butter. Press 1 heaping tablespoon into each liner and press down firmly. Bake for 5 minutes. Set aside.
- Beat cream cheese until smooth. Add sugar, sour cream, vanilla, and salt. Mix well, then beat in the egg until just combined. Spoon evenly over crusts (about 2 tablespoons each).
- Toss diced apples with brown sugar, cinnamon, and lemon juice. Spoon over cheesecake layer.
- In a small bowl, combine oats, flour, brown sugar, cinnamon, and salt. Cut in butter with a fork until crumbly. Sprinkle over apples.
- Bake for 20–22 minutes until centers are just set. Cool in pan, then refrigerate at least 2 hours.
Nutrition
Notes
Tips
- Spray the cupcake liners with non-stick baking spray so the cheesecakes release easily after chilling.
- Use a cookie scoop to portion the cheesecake batter evenly for uniform mini cheesecakes.
- Let the cheesecakes cool completely, then chill for at least two hours so they set firmly before serving.
Storage & Make Ahead
- Store cooled cheesecakes in an airtight container in the refrigerator for up to 5 days.
- Freeze fully cooled cheesecakes in a single layer until firm, then wrap individually and keep in an airtight container for up to 2 months.
- For the best texture, thaw overnight in the refrigerator and serve chilled or allow to stand at room temperature for 10–15 minutes before serving.
Tried this recipe?
Let us know how it was!Food Safety Tips:
- Baked goods are done when they reach their recommended internal temperature—usually between 190–210°F (88–99°C), depending on the type. Always check the recipe for exact guidance.
- Use separate utensils and surfaces for raw ingredients, especially eggs, to prevent cross-contamination.
- Wash your hands thoroughly after handling raw dough or eggs.
- Avoid leaving baked goods or raw dough at room temperature for extended periods.
- Never leave the oven unattended while baking.
- Choose oils with a high smoking point to minimize the release of harmful compounds.
- Ensure good ventilation when using a gas stove when using an oven or gas stove to maintain a safe cooking environment.
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