Yield: 9″ apple pecan pie cheesecake // Total Time: 2 hr. 30 min. + 9 hr. chilling time // Disclaimer: This post includes affiliate links. //

Say hello to the BEST fall cheesecake.

apple pecan pie cheesecake

Hello hello! Today we’re combining three fall classics into one: apple pie, pecan pie, and cheesecake. This is the perfect cheesecake for this Thanksgiving and fall in general. First of all, it has a *super* rich and creamy cheesecake base. Baked inside is a spiced apple pie filling, and on top is a crunchy pecan pie topping. It’s rich, creamy, sweet, salty, crunchy dessert perfection.

There are quite a few steps to this cheesecake but the great news is it’s the perfect make-ahead dessert since you’ll have to chill the cheesecake for at least 8 hours before serving. Below you’ll find some tips and tricks that (I hope) are helpful for getting the perfect cheesecake. Happy baking!

recipe tips

weigh your ingredients

Weighing your ingredients is important for getting the recipe perfect and getting consistent results. I do provide cup measurements but please note that I test all my recipes in grams and can not guarantee that your bake will turn out like mine. This kitchen scale is super cheap and a great starter scale!

room temperature ingredients

While it’s almost always important to have room temperature ingredients so all your ingredients come together, it’s ESPECIALLY important when it comes to cheesecake. Be sure to take out your cream cheese, heavy cream, and eggs at least 1 hour, and up to 2 hours before starting the recipe.

how to avoid cracks in a cheesecake

Here are my 3 best tips for avoiding cracks in your cheesecake –

1. mix the batter carefully

After adding in the eggs, you’ll want to make sure to only mix the batter until the eggs are fully incorporated. This will make sure we don’t add too much air into the batter, which will help keep the batter dense and avoid cracks forming on top.

2. bake your cheesecake in a water bath

It’s really the best way to ensure you get an evenly cooked cheesecake, and no cracks on top. To make a water bath, you’ll just place your cheesecake pan in a larger pan, and fill that pan with hot water right before baking the cheesecake. If you’re worried about the integrity of your springform pan and any leaking, wrap aluminium foil around the sides of your cheesecake pan (keeping the top of the pan exposed) before placing it in the larger pan. A lasagna pan (15×10) is the perfect size to use for a water bath for a 9″ cheesecake – I picked up just a simple $7 one from Walmart for this cheesecake!

3. cool the cheesecake in the oven

Once your cheesecake is done baking, turn off the oven and leave the door of the oven just *slightly* ajar. Let the cheesecake sit like that for one hour before transferring it to the fridge. This process allows your cheesecake to slowly come down to room temperature rather than quickly going from 350F to room temperature, which makes it less likely that the top will crack.

how to tell when a cheesecake is done baking

Cheesecake is done baking when it’s only slightly wobbly in the center. I like to temp my cheesecake as a more accurate way to tell when it’s done. A thermometer stuck into the middle of the cheesecake should read 170 fahrenheit / 76 celsius.

the cheesecake needs to set for a while

The most unfortunate thing about cheesecake is that it needs to set. Ideally you’ll want to bake the cheesecake at night to be served the next day, because it will need to set in the fridge for at least 8 hours.

ingredients and substitutions

For the shortbread crust:

Unsalted butter: salted or your favorite non-dairy butter stick will work perfectly here as well.

Light brown sugar: for flavor and sweetness. Dark brown sugar will work perfectly as well.

All purpose flour: for structure.

Pecan flour: for a little bit of pecan flavor in the crust! You can omit this and replace it with all purpose flour, or make your own pecan flour by grinding up pecans in a food processor.

Salt & apple pie spice: for flavor.

For the apple pie filling:

Apples: use your favorite baking apple here! I used a combination of granny smith and honeycrisp. You can also use fuji, gala, jonathan, or braeburn!

Lemon juice: fresh or bottled will work here. Helps to prevent browning and brings out the flavor of the apples.

Light brown sugar: for sweetness and a bit of flavor.

Apple pie spice: use a blend of apple pie spice to really get those classic warm apple pie spices in the filling. You can also make your own blend, or use more cinnamon.

Cornstarch & water: a little corn starch slurry helps thicken up the apple pie filling.

For the cheesecake:

Cream cheese: the base of the cheesecake and what makes it tangy, rich, and creamy.

Eggs: binds the batter together.

Granulated sugar: for sweetness and helps lock in moisture.

Corn starch: for thickening up the cheesecake. You can substitute in 2 tbsp. of flour in its place if needed.

Heavy whipping cream: for moisture and richness. You could use sour cream in its place as well.

Vanilla: for flavor.

For the pecan pie topping:

Crushed pecans: the star of any pecan pie!

Unsalted butter & heavy whipping cream: for thickening the mixture and for richness. You can use salted butter, just be sure to omit the extra salt from this part.

Light brown sugar: for sweetness and flavor.

Salt: for flavor.

how to make apple pecan pie cheesecake

Here are some shots of the process of making this apple pecan pie cheesecake. You can find the full recipe at the end of this blog post!

  • Wash, peel, and dice up your apples into small cubes.
  • Cook the apples with the sugar, apple pie spice, and lemon juice until softened, then whisk in the cornstarch slurry until the mixture is thickened. Set aside to cool while you make the crust and filling.
  • Combine all of the pecan shortbread crust ingredients in a small mixing bowl.
  • Pat the crust down into a springform pan and bake for 10 minutes.
  • Beat together the cream cheese, sugar, and cornstarch until light and fluffy.
  • Beat in the eggs and vanilla until just combined.
  • Beat in the heavy cream until just combined.
  • Pour 1/2 of the cheesecake batter over the baked crust, then top with the apple pie filling. Top with the remaining cheesecake batter, then bake.

apple pecan pie cheesecake q&a

what size cake pan do I need?

You’ll need a 9″ springform pan for this cheesecake. You can use a 10″ springform, just note that your cheesecake will be thinner and will require a little less bake time. I wouldn’t recommend using a non-springform pan because it will be more difficult to get the cheesecake out of the pan, but if you’re okay with just serving the cheesecake from the pan, then a non-springform pan will work.

how should I store this cake?

This cheesecake needs to be stored in the fridge. I would recommend serving it no more than 2-3 days after baking, but it will keep for a week.

why do you measure in grams?

My recipes are all written in grams because it is the most accurate way to bake. When you use a kitchen scale, you ensure that your baked goods turn out as close to the written recipe as possible. Plus, the cleanup is way easier when using a scale! I will provide standard cup measurements but please note that I have not tested the recipe using cup measurements and therefore can not guarantee your recipe will come out how mine did. Here is my favorite kitchen scale

a note on oven temperature

Ovens vary and fluctuate in temperature and aren’t always at the temperature they claim to be. If you love to bake like I do, I highly recommend getting an oven thermometer. They are super helpful for letting you know when your oven might be lying to you! I use this one.

tools and ingredients

You can find all my favorite tools and ingredients that I use on my Amazon Storefront page, here!

did you make this apple pecan pie cheesecake?

If you made this apple pecan pie cheesecake I would love to see it and know your thoughts! Please leave a comment and review down below, and tag me on Instagram @freshbeanbakery. If you have any questions about the recipe I will gladly do my best to answer them in the comments below!

Apple Pecan Pie Cheesecake

4.93 from 13 votes
Creamy, rich cheesecake with a pecan shortbread crust, apple pie filling, and pecan pie topping.
Prep Time1 hour
Cook Time1 hour 30 minutes
Chilling/Resting Time 9 hours
Total Time11 hours 30 minutes
Servings1 9″ cheesecake


Apple Pie Filling

  • 5 small apples*
  • 1 tbsp. lemon juice
  • 50 g light brown sugar (¼ c.)
  • 1 tbsp. apple pie spice
  • 1 tbsp. cornstarch
  • 1 tbsp. water

Pecan Shortbread Crust

  • 90 g unsalted butter (6 ⅓ tbsp.)
  • 100 g light brown sugar (½ c.)
  • 120 g all purpose flour (1 c.)
  • 30 g pecan flour (¼ c. + 2 tbsp.)
  • 1 tsp. apple pie spice


  • 675 g cream cheese room temperature (3 bricks)
  • 225 g granulated sugar (1 c. + 2 tbsp.)
  • 1 ½ tbsp. cornstarch
  • 3 eggs room temperature
  • 2 tsp. vanilla
  • 170 g heavy whipping cream room temperature (⅔ c.)
  • 1 tbsp. lemon juice

Pecan Pie Topping

  • 56 g unsalted butter (¼ c.)
  • 100 g light brown sugar (½ c.)
  • 75 g heavy whipping cream (⅓ c.)
  • tsp. salt
  • 170 g crushed pecans (1 ½ c.)


Apple Pie Filling

  • Rinse off your apples, then peel them and dice them into ~1" squares.
  • Add the apples, lemon juice, sugar and apple pie spice to a medium saucepan set over medium heat and bring to a simmer.
  • Cook for 5 minutes, or until the apples soften a little.
  • In a small bowl, whisk together the cornstarch and water. While constantly stirring the apples, mix in the cornstarch slurry. Continue to cook until the mixture is thickened, then remove the apples from the heat.**

Pecan Shortbread Crust

  • Preheat the oven to 350°F / 175°C. Line the bottom of a 9" springform pan with parchment paper by placing the paper on the base, then snapping the pan together.
  • In a small mixing bowl, melt the butter. Mix in the sugar, flour, pecan flour, and apple pie spice until you have a cohesive dough.
  • Press the crust into the bottom of the springform pan, and bake for 10 minutes. In the meantime, make the cheesecake filling.


  • Add the cream cheese, sugar, and cornstarch to a large mixing bowl (or to a stand mixer fitted with the paddle attachment.)
  • Use a hand mixer (or stand mixer) to beat the ingredients together for 2 minutes.
  • Add the three eggs and vanilla into the cream cheese, and beat the mixture on low speed *just* until the eggs have been fully incorporated.
  • Add in the heavy cream and lemon juice, and again beat on low speed just until the mixture is cohesive.
  • Pour ½ of the cheesecake filling over the crust. Carefully spoon heaps of the apple pie filling over the cheesecake to make an even layer, then top it off with the remaining cheesecake batter.
  • Tap the pan on the counter a few times to help remove any air from the filling.
  • Fill a 10×15" baking dish, or any larger pan that can reasonably fit the 9" springform inside of it, a third of the way with hot water. If desired, wrap tin foil around the bottom of your springform pan to avoid the possibility of water seeping into the springform.
  • Place the springform pan into the larger pan, then place the whole thing into the oven. Bake for 70-80 minutes, or until the cheesecake only slightly wobbles and reaches an internal temperature of at least 170°F / 76°C. If the cheesecake starts to brown on top, gently place a piece of tinfoil over the top of the pan.
  • Once the cheesecake is fully cooked, turn off the oven and leave the door slightly ajar with the cheesecake in it for 1 hr. before transferring it to the fridge to chill for at least 8 hours.

Pecan Pie Topping

  • (Save this step for until you're ready to serve the cheesecake!)
  • Add the butter, sugar, heavy cream, and salt to a small saucepan. Set the mixture over medium heat, and stir it ocasionally until everything is melted and smooth.
  • Bring the mixture to a boil, and let it boil for 2 minutes. Remove it from the heat and immediately stir in the pecans.
  • Let the topping cool down on the side for 5 minutes, then smooth it out to an even layer on top of the cheesecake.*** Slice, serve, and enjoy!


*I used a mixture of granny smith and honey crisp, feel free to use your favorite baking apple(s)!
**You can make this ahead of time and store it in an airtight container in the fridge for 3-4 days before baking the cheesecake.
***Alternatively, you can slice the cheesecake and then top the slices with the pecans which will be easier. You’ll want to slice and serve the cheesecake right after placing the pecans on top. In order to slice through the pecans without crushing the cheesecake, place your knife on top of where you want to slice, then kind of wiggle it around to create a small line that doesn’t have any pecans. Slice, repeat for all slices, then serve and enjoy!

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Recipe Rating


    1. Hi! This cheesecake can be made 2-3 days ahead of time and kept in the fridge. If you’re looking for longer term storage – I haven’t tried freezing it but looking around it seems that you should be able to safely freeze it for up to 1 month. I’d recommend not making the topping until you want to serve the cheesecake. When you want to serve the cheesecake, put it in the fridge to defrost the night before serving. Hope this helps! 🙂

  1. Hi Erin,

    Can I put the topping on sooner rather than later? You said to wait until ready to serve but is it something that can be done earlier c

    1. Hi, if you want to put the topping on a while before serving I’d recommend slicing the cheesecake & then putting the pecan topping on so that slicing is easier. Hope this helps! 🙂

  2. 4 stars
    Hi – instead of pecan flour can i use almond flour? Also for the apple spice, if ireplace it with just cinnamon, how much should i add?

    1. Hi, you can definitely use almond flour instead! And using cinnamon instead of apple pie spice would just be a 1:1 swap. Hope you enjoy! 🙂

  3. 5 stars
    Hi Erin! Baking this cheesecake as I type this! Was wondering if I can bake instead of doing the water bath? My cheesecake is currently in the oven with water bath and it’s been 70minutes and it’s still pretty soft. Would it be fine if I bake as an alternate? Please let me know soon!

    1. Hi Dez! Thanks so much for making the recipe! Sorry I couldn’t respond right away so I hope everything turned out. I’m sorry but I’m not sure what you mean by bake instead of the water bath, the cheesecake bakes in the oven with the pan in the water bath. You could bake it without a water bath but you’d run a greater risk of uneven cooking and the cheesecake cracking. My cheesecake took about 80 minutes to reach 170F and be done baking. I always recommend having an oven thermometer as your oven may be a lower temperature than it claims to be which can result in the bake taking longer. Also, checking the cheesecake for doneness with a thermometer is a sure-fire way to make sure it’s done baking. I hope this helps!

  4. Looks delicious! Will be trying this next week! Question: would it be okay to apply the pecan topping, serve, and then refrigerate leftovers with the topping? I’m curious if the topping hardens too much if refrigerated

    1. Hi Lori, thank you so much! You can store the sliced pieces with the pecan topping in the fridge. It will harden but shouldn’t be too difficult to eat! The hardening is more of a problem for first cutting the cheesecake, as it will crush the cheesecake underneath it which isn’t as pretty for serving. I hope you love the recipe! 🙂