Pecan pie has always been one of my favorite desserts, but the traditional version is loaded with far too much sugar.
That is why I started making these keto pecan pie cheesecake cups instead. They give you the same sweet, nutty crunch without taking you off track.

Because they are made in a muffin tin, you get neat single servings that are easy to grab and enjoy.
This dessert is completely low carb and keto friendly, which means you can stick to your eating plan without feeling deprived.
They look impressive on a plate, but the whole process is simple and straightforward to make at home.
Why I Love This Recipe
Two Classics in One – You get the rich taste of pecan pie and creamy New York cheesecake in one amazing low carb bite.
Real Gooey Caramel – Using allulose creates a true, sticky caramel topping that never gets gritty or crystallizes in the fridge.

No Water Bath Needed – Baking these in a standard muffin tin skips the annoying water bath and prevents any ugly cheesecake cracks.
Ultra Creamy Texture – A touch of sour cream makes the keto cheesecake layer extra smooth, velvety, and ridiculously rich.
Ingredients You’ll Need
For The Crust
- 1 CUP Almond Flour
- 1/4 CUP Powdered Allulose
- 1/4 TSP Fine Sea Salt
- 4 TBSP Unsalted Butter, Melted
For The Cheesecake
- 16 OZ Cream Cheese, Softened
- 1/2 CUP Powdered Allulose
- 2 Large Eggs
- 1/4 CUP Sour Cream
- 1 TSP Vanilla Extract
For The Pecan Topping
- 1 CUP Pecans, Chopped
- 3 TBSP Unsalted Butter
- 1/3 CUP Allulose
- 1/3 CUP Heavy Cream, Warmed
- 1/2 TSP Vanilla Extract
- 1/4 TSP Fine Sea Salt
How To Make
Step 1
Heat the oven to 325°F and line 12 muffin cups with paper liners. Mix the almond flour, powdered allulose, salt, and melted butter, then divide the crumbs among the cups and press them down firmly.
Step 2
Bake the crusts for 6 minutes. Let them cool while you prepare the cheesecake.
Step 3
Beat the cream cheese and powdered allulose until smooth. Mix in the eggs one at a time, then blend in the sour cream and vanilla.
Step 4
Divide the filling among the cups and bake for 17 to 20 minutes, until the edges are set and the centers still have a slight jiggle. Cool completely, then refrigerate for at least 2 hours.
Step 5
Toast the chopped pecans in a dry skillet over medium-low heat for 3 to 4 minutes, stirring often, then transfer them to a plate.
Step 6
Melt the butter in the skillet, stir in the allulose, and cook until light amber. Slowly stir in the warm heavy cream, then add the vanilla, salt, and toasted pecans and cook for 1 minute more.
Step 7
Let the pecan topping cool until thick but spoonable, then mound it over the chilled cheesecake cups and serve.

Tips
Watch the Caramel Heat Closely
Allulose browns much faster than regular sugar and can burn in just a few seconds. I recommend keeping your burner on medium-low the entire time you melt the butter and sweetener.
As soon as you notice a light amber color, take the skillet off the heat immediately. The residual heat in the pan will keep cooking the mixture.
Warm the Heavy Cream First
Pouring cold cream into hot melted butter and sweetener will cause the mixture to seize and separate. I always pop the cream into the microwave for about fifteen seconds until it feels warm to the touch.

When the cream is warm, it blends smoothly into the melted butter without splattering. This gives you a glossy and creamy caramel base for the pecans.
Mix the Filling on Low Speed
From my experience, whipping too much air into the batter makes the cheesecake cups puff up in the oven and collapse in the middle as they cool.
Keep your hand mixer on the lowest speed once you add the eggs. You just want to blend everything together until smooth without creating excess bubbles.
More Recipes
FAQ
Can I replace the allulose with an erythritol blend like Swerve?
You can use an erythritol blend in the crust and cheesecake filling, but it does not work well in the pecan topping.
Allulose melts and caramelizes into a smooth syrup, while erythritol recrystallizes into a crunchy, gritty texture once the topping cools.
Keto Pecan Pie Cheesecake Cups
Equipment
- muffin pan
- hand mixer
Ingredients
For The Crust
- 1 CUP Almond Flour
- 1/4 CUP Powdered Allulose
- 1/4 TSP Fine Sea Salt
- 4 TBSP Unsalted Butter, Melted
For The Cheesecake
- 16 OZ Cream Cheese, Softened
- 1/2 CUP Powdered Allulose
- 2 Large Eggs
- 1/4 CUP Sour Cream
- 1 TSP Vanilla Extract
For The Pecan Topping
- 1 CUP Pecans, Chopped
- 3 TBSP Unsalted Butter
- 1/3 CUP Allulose
- 1/3 CUP Heavy Cream, Warmed
- 1/2 TSP Vanilla Extract
- 1/4 TSP Fine Sea Salt
Instructions
- Heat the oven to 325°F and line 12 muffin cups with paper liners. Mix the almond flour, powdered allulose, salt, and melted butter, then divide the crumbs among the cups and press them down firmly.
- Bake the crusts for 6 minutes. Let them cool while you prepare the cheesecake.
- Beat the cream cheese and powdered allulose until smooth. Mix in the eggs one at a time, then blend in the sour cream and vanilla.
- Divide the filling among the cups and bake for 17 to 20 minutes, until the edges are set and the centers still have a slight jiggle. Cool completely, then refrigerate for at least 2 hours.
- Toast the chopped pecans in a dry skillet over medium-low heat for 3 to 4 minutes, stirring often, then transfer them to a plate.
- Melt the butter in the skillet, stir in the allulose, and cook until light amber. Slowly stir in the warm heavy cream, then add the vanilla, salt, and toasted pecans and cook for 1 minute more.
- Let the pecan topping cool until thick but spoonable, then mound it over the chilled cheesecake cups and serve.