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    Home » Dessert Recipes

    Mini Apple Pie Cheesecakes

    Published: Nov 4, 2022 · Modified: Aug 15, 2023 by Jennifer Brown · This post may contain affiliate links · 2 Comments

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    These mini apple pie cheesecakes have a soft almond flour crust, a creamy cinnamon cheesecake filling, and a topping of apples cooked in honey and spices! This healthier cheesecake recipe is SCD, gluten free, grain free, and refined sugar free.

    An apple cheesecake cupcake on a white plate.

    I love a good apple pie and I love a decadent cheesecake, so I created this incredible apple pie cheesecake to be the best of both worlds!

    The farmer cheese filling is so creamy and the combination of spices and sweetness is spot on.

    Their small size means these cheesecakes bake in the oven and set faster in the refrigerator.

    It also means no need to slice and that leftovers can be easily frozen!

    It really is a perfect fall cheesecake recipe!

    How to make your farmer cheese creamy

    Farmer cheese, which is also known as dry curd cottage cheese, is almost like a very dry and much grittier ricotta cheese.

    Several apple cheesecake bites on a large white plate.

    To turn this low lactose cheese into a smooth and creamy cheesecake filling you need to:

    • Make sure all the filling ingredients are at room temperature before blending.
    • Blend the cinnamon cheesecake filling really well. I highly suggest using a high speed blender like a Vitamix or Blendtec.
    • Don't overbake. The cheesecakes are done once the sides have set and the center inch is a bit wobbly.
    • Leave the oven door closed during the first 12 minutes of baking to help avoid cracking.

    Ingredients and directions for cheesecake apple topping

    Ingredients for the stewed apples on a pink table.

    Apples - I chose gala apples because of their natural sweetness, however, feel free to use any red apples you'd like. I don't suggest using Granny Smith because their tart flavor.

    Butter - If you prefer, ghee or coconut oil can be used instead.

    Begin by peeling, coring, and dicing the apples into small chunks (photo 1).

    Heat the honey and butter in a large pot over medium heat (photo 2).

    Four photos showing how to make the stewed apples.

    Once the butter has melted, add the apples to the pot and sprinkle the spices on top (photo 3).

    Give the mixture a good stir and continue to cook over medium heat, stirring occasionally, until the apples have softened and the liquid in the pot has almost disappeared (photo 4).

    Transfer the apples to a glass container and allow to cool completely before topping the apple cheesecake bites.

    Tip:

    Make the cheesecake apple topping first or the day before serving to give enough time to cool completely and to allow the flavors to meld together. Simply store in an airtight container in the refrigerator.

    Crust ingredients and directions

    Ingredients for the almond flour crust on a pink table.

    Almond Flour - Blanched finely ground almond flour works best for this recipe, but cashew flour can also be used.

    Melted Butter - Melted ghee or coconut oil can be used instead.

    In a medium bowl, add the almond flour, ground cinnamon, honey, and melted butter (photo 5).

    Mix and press together until all of the almond flour is wet (photo 6).

    The dough will be crumbly in texture but should stick together when pressed.

    Four photos showing how to make the almond flour crust.

    Evenly distribute the dough among the twelve lined muffin cups.

    I suggest using the JUMBO size liners so that each cheesecake can have lots of filling!

    If you don't use the JUMBO liners, you'll probably have some leftover cheesecake filling.

    Just pour the leftover filling into a small oven safe ramekin and bake alongside the rest of the mini apple cheesecakes.

    You'll end up with a delicious, custard like dessert!

    Use a tart tamper (like the one shown in the photo above) or your fingers to press the dough into the bottom of the cups (photo 7).

    Bake in the oven just until the crust is golden brown in color (photo 8).

    Allow to cool before pouring in the cinnamon cheesecake filling.

    Filling ingredients

    Ingredients for the cheesecake filling on a pink table.

    Farmer Cheese - Also known as dry curd cottage cheese, it can typically be found in the dairy section of the grocery store. If following the SCD diet, I believe the Friendship Dairies brand is the only one currently allowed. You could also strain SCD yogurt for 24 hours in the refrigerator until it's the consistency of traditional cream cheese and use it in place of farmer cheese. If you do not follow the SCD diet, then feel free to use traditional cream cheese.

    Filling directions

    Ensure all of the cinnamon cheesecake filling ingredients are at room temperature before placing in the blender jar.

    Add the eggs and honey first to make sure they are closest to the blades.

    Ingredients for the cinnamon cheesecake in the blender.

    Blend on high speed until the filling is smooth with no visible lumps, scraping down the sides of the jar as needed.

    Evenly pour the mixture into the prepared muffin cups, filling until almost to the very top.

    The baked cheesecakes in the muffin liners.

    Bake the cheesecakes on the second rack from the bottom for about 10 minutes.

    The apple pie cheesecake bites are done when the sides are set and the middle is slightly wobbly.

    Turn the oven off and crack the door, leaving the cheesecakes inside for an additional 10 minutes.

    Allow to cool on the counter completely before wrapping the muffin tin with plastic wrap and placing in the refrigerator for 3 to 4 hours or overnight.

    Once the cheesecakes have completely set, remove the plastic wrap and gently peel the liner off.

    An overhead view of the cheesecakes on a white plate.

    Top each cheesecake you plan on serving with a generous spoonful of stewed apples and a light dusting of freshly grated cinnamon.

    How do I store the mini apple pie cheesecakes?

    I suggest storing the stewed apple topping in an airtight container in the refrigerator separate from the cheesecakes.

    Topping the cheesecakes with the apples and storing together tends to make the cheesecakes a bit soggy.

    Cover the cinnamon cheesecakes with plastic wrap and store in the refrigerator for three to five days.

    The mini cheesecakes can also be individually wrapped in plastic wrap and then aluminum foil and stored in the freezer for up to one month.

    When you're ready to eat one, simply thaw in the refrigerator overnight or on the counter for a few hours.

    A gluten free apple cheesecake on a white plate with a forkful taken out of it.

    Here are more healthy fall treats you'll love!

    • Mini Pumpkin Cheesecakes
    • Cranberry Orange Muffins
    • Upside-Down Pear Cake
    • Cranberry Apple Crumble

    If you’ve made this recipe, please leave a comment and star rating below! This is the best way to help support me and this blog!

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    Recipe inspired by my Mini Pumpkin Cheesecakes recipe.

    Recipe

    A mini apple pie cheesecake on a white plate with more in the background.

    Mini Apple Pie Cheesecakes

    by: Jennifer Brown
    These mini apple pie cheesecakes have a soft almond flour crust, a creamy cinnamon cheesecake filling, and a topping of apples cooked in honey and spices! This healthier cheesecake recipe is SCD legal, gluten free, grain free, and refined sugar free.
    Print Recipe Pin Recipe Save Recipe Saved!
    Prep Time 15 minutes mins
    Cook Time 20 minutes mins
    Apple Topping 30 minutes mins
    Course Dessert
    Cuisine American
    Servings 12
    Calories 282 kcal

    Ingredients
      

    Apple Topping

    • 2 pounds apples any sweet apples will work
    • ¼ cup honey
    • 2 Tablespoons unsalted butter
    • ½ teaspoon ground cinnamon
    • ⅛ teaspoon ground nutmeg
    • ⅛ teaspoon allspice

    Crust

    • 1 cup blanched finely ground almond flour
    • 1 teaspoon ground cinnamon
    • 2 Tablespoons melted unsalted butter
    • 1 teaspoon honey

    Cinnamon Cheesecake Filling

    • 22 ounces farmer cheese at room temperature
    • 3 large eggs at room temperature
    • ½ cup honey
    • 1 teaspoon vanilla extract
    • 1 Tablespoon ground cinnamon

    Instructions
     

    Apple Topping

    • Peel, core, and dice the apples.
    • Heat the butter and honey in a large pot over medium heat. Once the butter has melted, add the apples and spices.
    • Stir the mixture until well combined and continue cooking over medium heat, stirring occasionally, until the apples are tender and the liquid in the pot has mostly disappeared.
    • Allow the apples to cool completely before topping the cheesecakes.

    Crust

    • Preheat the oven to 325F and line a standard muffin tin with jumbo liners. Set aside.
    • In a medium bowl, mix and press the crust ingredients together until all of the almond flour is wet.
    • Fill each muffin cup with about 1 Tablespoon of dough and use either a tart tamper or your fingers to press the dough into the bottom of the cups.
    • Bake for 8 to 10 minutes on the rack second from the bottom. The crusts should be a light golden brown color when done. Allow to cool before pouring the cheesecake filling on top.

    Cinnamon Cheesecake Filling

    • While the crusts are baking, place the filling ingredients in the jar of a blender, making sure the eggs and honey are closest to the blades.
    • Blend on high speed until the filling is smooth with no visible lumps.
    • Pour the filling into each cup, filling to almost the very top.
    • Place the pan on the rack second from the bottom to bake.
    • The cheesecakes will bake for 10 to 12 minutes just until the sides have set and the center inch of the cheesecakes wobbles slightly when the pan is gently jiggled.
    • Turn off the oven. Crack the oven door, leaving the cheesecakes inside for 10 minutes.
    • Allow to cool completely on the counter before wrapping the muffin tin in plastic wrap and transferring to the refrigerator for a minimum of 3 to 4 hours to completely set.
    • Before serving, peel the liners from the cheesecakes. Add the apple topping only to the cheesecakes you're planning on eating and garnish with a light dusting of cinnamon.

    Notes

    • I like to make the apple topping the day before I plan to serve the cheesecakes, this allows the flavors to really meld together. 
    • I don't suggest placing the apple topping on any leftover cheesecakes, as they tend to become soggy. 
    • Leftovers can be wrapped in plastic wrap and stored for 3 to 5 days in the refrigerator. The post above has directions for how to freeze and defrost the cheesecakes and the apple topping.
     
    The nutritional information calculated in this recipe are just an estimate. The photos and content above are copyright protected. Please do not use my photos. Please do not copy this recipe and share it on your own website or social media channels. If you wish to tell people about this recipe, you can provide a link back to my blog rather than copying the recipe. Thank you! XO, Jen

    Nutrition

    Calories: 282kcal | Carbohydrates: 31g | Protein: 11g | Fat: 14g | Saturated Fat: 6g | Polyunsaturated Fat: 0.4g | Monounsaturated Fat: 1g | Cholesterol: 74mg | Sodium: 228mg | Potassium: 115mg | Fiber: 3g | Sugar: 26g | Vitamin A: 228IU | Vitamin C: 4mg | Calcium: 43mg | Iron: 1mg
    Keyword apple cheesecake bites, mini apple cheesecakes, mini apple pie cheesecakes
    Did you make this recipe?Let me know how it was by leaving a comment and star rating below!

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    1. Laura

      August 20, 2023 at 9:11 am

      Farmer cheese is similar to tvorog cheese?

      Reply
      • Jennifer Brown

        August 26, 2023 at 10:42 am

        Yes it is.

        Reply

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