There’s something magical about the way certain flavors instantly transport us back to cherished memories. For me, nothing evokes the feeling of home quite like the warm, comforting aroma of apple pie wafting through the kitchen. But what happens when you combine that classic taste with the creamy decadence of cheesecake and the convenient portability of cookies? Pure dessert bliss!
Today, I’m excited to share my recipe for Apple Pie Cheesecake Cookies—a delightful treat that brings together three beloved desserts in one irresistible package. These cookies feature a buttery, cinnamon-spiced base with a luscious cheesecake filling and a crown of caramelized apples. They’re perfect for holiday gatherings, bake sales, or simply treating yourself to something special on a cozy evening.
Why You’ll Love These Cookies
I’ve been perfecting this recipe for years, and there are so many reasons why these cookies have become a staple in my baking repertoire:
- They combine three classic desserts into one perfect bite
- The textures are divine—crisp edges, tender centers, creamy filling
- You can make components ahead of time for easy assembly
- They’re impressive enough for special occasions but simple enough for everyday baking
- The aroma while baking will make your home smell like a gourmet bakery
Ingredients Breakdown
Let’s take a closer look at what goes into these magnificent cookies:
For the Cookie Base:
- 2½ cups all-purpose flour
- ½ teaspoon baking powder
- ½ teaspoon salt
- 1 teaspoon ground cinnamon
- ¼ teaspoon ground nutmeg
- 1 cup unsalted butter, softened
- ¾ cup granulated sugar
- ¼ cup brown sugar, packed
- 1 large egg
- 2 teaspoons vanilla extract
For the Cheesecake Filling:
- 8 oz cream cheese, softened
- ¼ cup granulated sugar
- 1 large egg yolk
- 1 teaspoon vanilla extract
- 1 tablespoon all-purpose flour
For the Apple Topping:
- 2 medium apples (preferably Honeycrisp or Granny Smith)
- 2 tablespoons unsalted butter
- ¼ cup brown sugar
- 1 teaspoon ground cinnamon
- ¼ teaspoon ground nutmeg
- 1 tablespoon lemon juice
- 1 tablespoon cornstarch
For the Streusel Topping (Optional):
- ½ cup all-purpose flour
- ¼ cup brown sugar, packed
- ¼ cup old-fashioned oats
- ¼ teaspoon ground cinnamon
- ¼ cup cold unsalted butter, cubed
Essential Equipment
Before we dive into the baking process, make sure you have these tools on hand:
- Stand mixer or hand mixer
- Large mixing bowls
- Medium saucepan
- Cookie scoop (about 2 tablespoons capacity)
- Silicon spatula
- Measuring cups and spoons
- Baking sheets
- Parchment paper or silicone baking mats
- Wire cooling rack
- Small bowl for the cheesecake filling

Step-by-Step Instructions
Preparing the Cookie Dough
- In a medium bowl, whisk together the flour, baking powder, salt, cinnamon, and nutmeg. Set aside.
- In the bowl of a stand mixer fitted with the paddle attachment (or using a hand mixer), cream together the butter, granulated sugar, and brown sugar until light and fluffy, about 3-4 minutes.
- Add the egg and vanilla extract to the butter mixture and beat until well combined, scraping down the sides of the bowl as needed.
- Gradually add the dry ingredients to the wet ingredients, mixing on low speed just until combined. Be careful not to overmix.
- Cover the dough with plastic wrap and refrigerate for at least 1 hour, or up to overnight. This chilling step is crucial for the best texture and flavor.
Making the Cheesecake Filling
- In a medium bowl, beat the softened cream cheese and sugar until smooth and creamy, about 2 minutes.
- Add the egg yolk and vanilla extract, beating until fully incorporated.
- Mix in the tablespoon of flour until just combined.
- Cover and refrigerate the filling while you prepare the apple topping.
Preparing the Apple Topping
- Peel, core, and dice the apples into small cubes (about ¼-inch pieces).
- In a medium saucepan over medium heat, melt the butter.
- Add the diced apples, brown sugar, cinnamon, nutmeg, and lemon juice. Stir to combine.
- Cook for about 5-7 minutes, until the apples begin to soften but still hold their shape.
- In a small bowl, mix the cornstarch with 1 tablespoon of water to create a slurry.
- Pour the cornstarch slurry into the apple mixture and continue cooking for another 1-2 minutes, until the mixture thickens.
- Remove from heat and allow to cool completely.
Optional Streusel Topping
- In a medium bowl, combine the flour, brown sugar, oats, and cinnamon.
- Add the cold, cubed butter and use your fingers or a pastry cutter to work the butter into the dry ingredients until the mixture resembles coarse crumbs.
- Refrigerate until ready to use.
Assembling and Baking the Cookies
- Preheat your oven to 350°F (175°C). Line baking sheets with parchment paper or silicone mats.
- Remove the cookie dough from the refrigerator and let it sit at room temperature for about 10 minutes to soften slightly.
- Using a cookie scoop or tablespoon, portion out the dough into 2-tablespoon balls and place them on the prepared baking sheets, leaving about 2 inches between each cookie.
- Use your thumb or the back of a measuring teaspoon to create an indentation in the center of each cookie.
- Fill each indentation with about 1 teaspoon of the cheesecake filling.
- Top the cheesecake filling with a small amount of the apple mixture.
- If using, sprinkle a bit of the streusel topping over each cookie.
- Bake for 12-15 minutes, or until the edges of the cookies are golden brown.
- Allow the cookies to cool on the baking sheets for 5 minutes before transferring them to a wire rack to cool completely.
Variations and Customizations
One of the things I love most about these cookies is how versatile they are. Here are some delicious variations I’ve tried over the years:
- Pear Pie Cheesecake Cookies: Substitute pears for apples and add a pinch of cardamom to the spice mix.
- Caramel Apple Pie Cheesecake Cookies: Drizzle with caramel sauce after baking.
- Maple Apple Pie Cheesecake Cookies: Replace some of the sugar with maple syrup in the apple topping.
- Gluten-Free Version: Use your favorite gluten-free flour blend in place of all-purpose flour (just watch the consistency of your dough).
- Vegan Adaptation: Use vegan cream cheese and butter substitutes, and replace eggs with flax eggs.
Storage and Make-Ahead Tips
These cookies are at their best when eaten within 2-3 days of baking, but they can be stored in an airtight container in the refrigerator for up to 5 days. The cheesecake element means they need to be kept cool.
For longer storage, you can freeze the baked cookies for up to 3 months. Thaw them overnight in the refrigerator before serving.
If you want to prep ahead, you can:
- Make the cookie dough and refrigerate for up to 3 days or freeze for up to 3 months.
- Prepare the apple topping up to 3 days in advance and store in the refrigerator.
- Make the cheesecake filling up to 2 days ahead and keep refrigerated.
Nutritional Information
I believe in transparency when it comes to indulgent treats. Here’s the approximate nutritional breakdown per cookie:
Nutrient | Amount per Cookie |
---|---|
Calories | 245 |
Total Fat | 14g |
Saturated Fat | 8g |
Cholesterol | 55mg |
Sodium | 105mg |
Total Carbohydrates | 28g |
Dietary Fiber | 1g |
Sugars | 16g |
Protein | 3g |
Note: Values are approximate and may vary based on specific ingredients and portion sizes.
Serving Suggestions
These cookies are absolutely delicious on their own, but I love elevating them for special occasions. Here are a few of my favorite serving ideas:
- Serve slightly warm with a scoop of vanilla ice cream for a decadent dessert.
- Pair with hot apple cider or mulled cider for a cozy fall treat.
- Create a cookie sandwich by placing a thin layer of additional cheesecake filling between two cookies.
- Add these to a holiday cookie platter for a showstopping centerpiece.
- Serve with a hot cup of chai tea or coffee for an afternoon pick-me-up.

Common Problems and Solutions
Even experienced bakers run into issues sometimes. Here are solutions to common problems you might encounter:
Cookie Dough Too Soft
If your cookie dough is too soft to work with, refrigerate it for an additional 30 minutes to an hour. Chilled dough is much easier to handle and will result in cookies that hold their shape better.
Cheesecake Filling Too Runny
Make sure your cream cheese is softened but not melted. If your filling seems too loose, add an extra teaspoon of flour and refrigerate for 30 minutes before using.
Apple Topping Too Watery
Cook the apple mixture a bit longer to reduce excess moisture. If it’s still too watery, add a little more cornstarch slurry (mix 1 teaspoon cornstarch with 1 teaspoon water).
Cookies Spreading Too Much
Ensure your baking sheets are cool before placing new batches of cookie dough on them. Hot baking sheets can cause the butter in the dough to melt too quickly, resulting in excessive spreading.
Cookies Browning Too Quickly
If the edges of your cookies are browning too fast, reduce the oven temperature by 25°F and cover the edges with small pieces of aluminum foil.
Expert Tips from My Kitchen to Yours
After years of perfecting this recipe, I’ve gathered some invaluable tips:
- Use room temperature ingredients for the cheesecake filling to ensure a smooth texture.
- Don’t skip the chilling time for the cookie dough—it’s crucial for developing flavor and texture.
- For the apple topping, choose a mix of sweet and tart apples for the best flavor balance.
- When making the thumbprint indentation, dip your thumb in a little flour first to prevent sticking.
- If the edges of your cookies crack when making the indentation, simply press them back together gently.
- For perfectly uniform cookies, use a cookie scoop rather than a spoon.
- Rotate your baking sheets halfway through baking for even browning.
- Allow the cookies to cool completely before storing to prevent sogginess.
Seasonal Adaptations
One of the reasons I love this recipe is its versatility throughout the year:
- Spring: Add a touch of lemon zest to the cheesecake filling for brightness.
- Summer: Substitute peaches for apples and add a pinch of ginger to the spice mix.
- Fall: Double down on the apple pie flavor with a mix of apple varieties and a dash of apple cider in the topping.
- Winter: Add a splash of bourbon to the apple topping and a sprinkle of coarse sugar on top for a festive touch.

Frequently Asked Questions
Q: Can I make these cookies ahead of time for a party? A: Absolutely! You can prepare all components up to 3 days in advance and assemble and bake the day of the event. Alternatively, bake the cookies up to 2 days ahead and store them in the refrigerator.
Q: What’s the best type of apple to use for the topping? A: I prefer a mix of sweet and tart apples. Honeycrisp, Granny Smith, and Pink Lady all work beautifully. Avoid softer varieties like McIntosh that might break down too much during cooking.
Q: Can I freeze these cookies? A: Yes! These cookies freeze well for up to 3 months. Thaw them overnight in the refrigerator before serving.
Q: My cookies are spreading too much during baking. What am I doing wrong? A: This usually happens when the dough isn’t chilled enough or your butter was too warm. Make sure to chill the dough for at least an hour, and if your kitchen is warm, work quickly when shaping the cookies.
Q: Can I make these without the cheesecake filling? A: While the cheesecake filling is what makes these cookies special, you could substitute with a simple cream cheese frosting or even a vanilla buttercream if preferred.
Q: How do I store leftover cookies? A: Because of the cheesecake element, these cookies should be stored in an airtight container in the refrigerator for up to 5 days.
Q: Can I make these gluten-free? A: Yes! Use a 1:1 gluten-free flour blend in place of the all-purpose flour. The texture might be slightly different, but they’ll still be delicious.
Q: Do I need to peel the apples? A: I recommend peeling the apples for the best texture in the topping, but if you prefer the rustic look and extra fiber, you can leave some of the peel on.
Q: Can I double this recipe? A: Absolutely! This recipe doubles well. Just make sure you have enough refrigerator space for chilling the dough and enough baking sheets.
Final Thoughts
There’s something deeply satisfying about creating a dessert that combines multiple favorite treats into one perfect bite. These Apple Pie Cheesecake Cookies represent the best of three worlds: the familiar comfort of apple pie, the creamy indulgence of cheesecake, and the portable convenience of cookies.
What I love most about baking these cookies is how they bring people together. I’ve seen faces light up at family gatherings, watched them disappear from holiday cookie exchanges, and received countless requests for the recipe. There’s simply something magical about the combination of flavors and textures that makes them irresistible.
Whether you’re an experienced baker looking for a new challenge or a novice wanting to impress, these cookies are well worth the effort. The components can be prepared separately and assembled when you’re ready, making them more manageable than they might seem at first glance.
So the next time you’re craving something special, something that combines the best of classic American desserts, give these Apple Pie Cheesecake Cookies a try. I promise they’ll become a favorite in your baking repertoire, just as they have in mine.
Happy baking!