Keto… apple pie… cupcakes?! Yes! These spiced low carb vanilla cupcakes are super moist and filled with a gooey apple pie center and topped with a thick swirl of fresh whipped cream. They’re keto-friendly, no-sugar-added, and only 4 net carbs each (including the filling and topping).
Why These Keto Apple Pie Cupcakes Are the Best
- Warm fall flavors – cinnamon, nutmeg, and ginger give the cupcakes that spiced apple pie vibe.
- Surprise filling – the gooey apple pie center makes every bite decadent.
- Whipped cream topping – instead of frosting, a fluffy swirl of whipped cream keeps them light yet indulgent.
Ingredients Breakdown
(See recipe card at the end of the post for full ingredient measurements and units.)
Coconut Flour
Keeps these cupcakes low-carb and high fiber, while giving them a soft, cake-like texture.
Sugar-Free Sweetener
Adds sweetness without sugar. Granulated for the cupcakes, powdered for the filling and whipped cream. I used an erythritol/monk fruit blend in the cupcakes and whipped cream, allulose in the apple pie filling.
Baking Powder & Salt
Ensures rise and balances the sweetness.
Spices (Cinnamon, Ginger, Nutmeg)
Classic apple pie spices that give warmth and depth. Or feel free to use a pre-mixed apple pie spice blend.
Avocado Oil
Keeps the cupcakes moist and tender.
Milk
Unsweetened dairy-free milk or whole milk both work.
Eggs
Help the cupcakes rise and bind the batter together.
Vanilla Extract
Adds cozy, sweet bakery flavor.
Green Apples
The star of the filling—peeled, diced, and simmered into gooey perfection. I used granny smith variety, but any apples you like should work.
Lemon Juice
Brightens up the apple flavor and keeps them from browning.
Butter
Richens the apple filling and adds that pie-like taste.
Heavy Cream
Used in both the filling and the topping for a luscious, creamy texture.
How to Make Keto Apple Pie Cupcakes
1. Make the Cupcakes
Preheat oven to 350°F. Line a muffin tin with paper liners. In a large bowl, stir together the dry ingredients. Add the wet ingredients and mix until combined. Divide the batter evenly and bake 20–22 minutes. Let cool.
2. Prepare the Apple Pie Filling
Toss diced apples with lemon juice and cinnamon. Melt butter in a saucepan over medium heat, then add the apples. Simmer for about 10 minutes until softened and thickened. Stir in the cream and cook another 2–3 minutes. Let cool.
3. Fill the Cupcakes
Cut a small circle into each cooled cupcake, then scoop out the center with a spoon. Spoon in the apple pie filling.
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4. Make the Whipped Cream
Beat heavy cream with an electric mixer until stiff peaks form. Add powdered sweetener to taste. Pipe or spoon generously over each cupcake.
5. Finish & Serve
Dust with extra cinnamon or spices of choice, and enjoy!
Tips for Success
- Cool completely before filling – otherwise the whipped cream will melt.
- Use allulose for the filling – it caramelizes beautifully without crystallizing.
- Whip cream cold – chilled cream whips faster and holds its shape better.
Keto Apple Pie Cupcake Variations
- Nutty crunch – sprinkle chopped pecans or walnuts on top of the whipped cream.
- Caramel drizzle – add a spoonful of sugar-free caramel sauce before topping with whipped cream.
- Full cake version – bake cake batter in an 8×8-inch cake pan (increase baking time by a few minutes), then top with apple pie filling and whipped cream and slice into individual slices!
FAQs
Coconut flour can’t be swapped 1:1 with any other flour, but you can use any other vanilla cupcake recipe you like, and just add the spices/filling/topping from this recipe.
In small amounts, they certainly can be. This recipe only uses a small amount of apple spread across 12 cupcakes, keeping the carb count very low per serving which allows most people to remain in ketosis. However, always do what works best for you, as this may not work for everyone.
After filling and topping, yes. The cupcakes themselves before filling and topping can be kept at room temperature for about 2 days.
Try These Keto Apple Pie Cupcakes!
If you love apple desserts, you absolutely have to try these keto apple pie cupcakes. They’re the perfect mix of warm spices, gooey apple filling, and fluffy whipped cream topping—all without any added sugar. If you love them, make sure to try my Low Carb Apple Pie Cheesecake as well! Please leave a star rating, comment below, and tag me on Instagram if you make them!
XO,
Sarah
Keto Apple Pie Cupcakes
Want to save this recipe? 💌
I’ll email this post to you, so you can come back to it later! -Sarah
Ingredients
Cupcakes
- ¾ cup coconut flour
- ½ cup granulated sugar-free sweetener
- 2 tsp baking powder
- ½ tsp salt
- 1 tsp cinnamon
- ¼ tsp ginger
- ¼ tsp nutmeg
- 6 tbsp avocado oil
- 1 cup unsweetened dairy-free milk or whole milk
- 4 large eggs
- 1 tsp vanilla extract
Apple Pie Filling
- 2 small green apples peeled, cored, and diced
- 1 tbsp lemon juice
- ½ tsp cinnamon
- 3 tbsp salted butter
- ¼ cup powdered sugar-free sweetener or allulose
- 2 tbsp heavy cream
Whipped Cream
- 1 ½ cups heavy cream
- 2 tbsp powdered sweetener
Instructions
- Preheat the oven: Set oven to 350°F and line a standard muffin tin with 12 paper liners.
- Mix the batter: In a large bowl, whisk together coconut flour, sweetener, baking powder, salt, and spices. Add avocado oil, milk, eggs, and vanilla. Stir until smooth.
- Bake the cupcakes: Divide the batter evenly between liners. Bake 20–22 minutes until a toothpick comes out clean. Allow to cool completely.
- Make the apple filling: Toss diced apples with lemon juice and cinnamon. In a saucepan over medium heat, melt the butter. Add apples and simmer about 10 minutes, stirring occasionally, until softened and thickened. Stir in the cream and cook another 2–3 minutes. Remove from heat and let cool.
- Fill the cupcakes: Cut a small circle out of the top of each cupcake and scoop out the center. Spoon in cooled apple pie filling.
- Whip the cream: Beat heavy cream with an electric mixer until stiff peaks form. Sweeten with powdered sweetener to taste.
- Assemble: Pipe or spoon whipped cream onto each cupcake, dust with cinnamon, and serve!
As an apple pie lover these are one of my favorite fall desserts!!
This was just a flavor and texture EXPERIENCE! Amazing for any dessert no matter being low carb…