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A mini pecan pie cheesecake with pecan pie caramel sauce dripping down the sides and a cooling rack with pecan pie cheesecakes in the background.

Grain-Free Mini Pecan Pie Cheesecakes

These mini pecan pie cheesecakes are gluten-free and grain-free with a spiced pecan crust and topped with a decadent pecan pie caramel sauce. Perfect for holiday entertaining!
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Course: Dessert
Cuisine: American
Prep Time: 10 minutes
Cook Time: 25 minutes
Resting Time: 1 hour
Total Time: 35 minutes
Servings: 12 servings
Calories: 315kcal
Author: Megan


For the Crust:

  • 1 cup pecans
  • 3 tablespoons brown sugar
  • 1 teaspoon ground cinnamon
  • 1/4 teaspoon ground nutmeg
  • 2 tablespoons butter (melted)

For the Cheesecake Filling:

  • 2 (8 oz) packages cream cheese (softened)
  • 2/3 cup granulated sugar
  • 1 teaspoon vanilla extract
  • 2 eggs
  • 2 teaspoons ground cinnamon
  • 1/2 teaspoon ground nutmeg

For the Pecan Pie Caramel Sauce:

  • 1 cup granulated sugar
  • 1/4 cup water
  • 1/2 cup heavy cream
  • 2 tablespoons butter
  • 1 teaspoon ground cinnamon
  • 1/4 teaspoon ground nutmeg
  • 1/8 teaspoon ground cloves
  • 1 teaspoon pure vanilla extract
  • pinch of sea salt
  • 1 cup pecans (toasted)


  • Preheat the oven to 350F. Line a muffin-tin with 12 paper muffin cups. Set aside. 
  • Add pecans to a food processor. Combine until finely processed. The consistency should be similar to sand. Some slightly larger pieces of pecans is fine, too. 
  • Pour pecans into a medium sized bowl. Add in brown sugar, cinnamon and nutmeg and stir to combine. Pour melted butter over the pecan mixture and mix until butter is dispersed and all of the pecan pieces are moist. 
  • Add about 1 heaping tablespoon of the pecan mixture to each muffin well. Press down with the bottom of a glass cup or a measuring cup to create a flat surface in the pecan crust. You want to press down pretty hard so that the crust sticks together. Set aside.
  • Add the cream cheese to a large bowl. With an electric mixer, beat for 2 minutes, until the cream cheese is smooth and light. Add in the sugar and beat for another 1-2 minutes until completely combined. 
  • Add in the eggs and vanilla extract and mix combined. 
  • Stir in the cinnamon and nutmeg until evenly dispersed. 
  • Using a spoon or cookie scoop (my favorite), portion out the cheesecake mixture between the 12 muffin cups. 
  • Bake at 350F for 20-22 minutes, until the tops are lightly browned. Remove from oven and let cool completely. Then set in the refrigerator for at least an hour, but overnight is better.
  • To make the pecan pie caramel sauce, combine granulated sugar and water in a small saucepan over medium heat. 
  • Swirl the pan to combine the sugar and water as the sugar melts (don't stir as it can cause crystallization). The sugar will melt completely and then the mixture will start to turn from clear to a very light brown to finally an amber. 
  • Once it reaches amber, take off from the heat. Immediately pour in the heavy cream and whisk to combine. The mixture will bubbly violently so be cafeful. Return to the heat and stir until smooth. 
  • Once smooth, remove from the heat and add in the butter, cinnamon, nutmeg, cloves, vanilla and sea salt and stir to combine. 
  • Let sit for about 5 minutes to cool slightly, and then stir in the pecans. Let cool completely. 
  • Store pecan pie caramel sauce in the refrigerator until ready to use. You can let it sit at room temperature to soften or reheat in the microwave for about 15 seconds. 
  • When ready to serve cheesecakes, pour pecan pie caramel sauce over each individual cheesecake. You can serve the cheesecakes in the paper muffin cups, but I like to remove those before serving for a beautiful preseneation. 


  •  There are a few ways you can toast nuts - either in the oven or on the stove. My preference is on the stove top,  because it's much quicker. 
  • To toast nuts on the stove, just place your nuts in a large skillet over medium heat. Let heat up and toast for a few minutes, stirring frequently to ensure they toast evenly and do not burn. There will be a warm, roasted pecan aroma in the air. Once you smell that, take them off the stove top and proceed with the recipe.
  • Use paper muffin liners to easily get the cheesecakes out of the muffin tin. I typically don't serve my mini cheesecakes with the muffin liners on. I unwrap just before serving.
  • Allow your cheesecakes to cool completely! Once they are out of the oven, let cool. Then, place them in the refrigerator for at least an hour. However, overnight works and makes these easy to make ahead for entertaining.


Calories: 315kcal | Carbohydrates: 34g | Protein: 2g | Fat: 20g | Saturated Fat: 5g | Cholesterol: 50mg | Sodium: 49mg | Potassium: 89mg | Fiber: 1g | Sugar: 31g | Vitamin A: 310IU | Vitamin C: 0.2mg | Calcium: 31mg | Iron: 0.6mg
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