These gluten-free apple pie cupcakes are deliciously moist and taste like a homemade apple pie. With warm spices, an apple pie filling and apple spiced buttercream frosting, they are the ideal Autumn treat.
Be sure to check out more of my gluten-free cupcake recipes including my passion fruit cupcakes with cream cheese frosting and my gluten-free lemon-blueberry cupcakes.
The cupcakes are moist and flavored with just a tad of cinnamon. The filling and frosting have lots of spice so, I include just a little in the cupcake part.
Normally I use oil for my cakes and cupcakes because it does a better job of making gluten-free baked goods moist. But since these are the base for an apple pie cupcake, I wanted to inject some buttery pie crust flavor. So the recipe includes a combination of butter for flavor and oil to make them moist, fluffy and a perfect base for fruit filling.
Because this recipe includes soft butter, it is very important that the eggs and milk are at room temp. If you add cold eggs or milk to creamed butter and sugar, the butter will harden and form lumps. So place cold eggs in a bowl of warm water for 10 minutes to take the chill off. Heat the milk in the microwave for 10-15 seconds.
My go-to flour for gluten-free baking is King Arthur Measure for Measure. It works very well in almost all of my recipes, is widely available and is the most affordable of the flours I’ve tested. Pamela’s All Purpose Artisan Blend is similar and works well too. Cup4Cup is another gluten-free flour that works in many recipes but it contains milk powder and I avoid most dairy. It is also quite pricy.
All three of these flours are certified gluten-free and contain binders like xanthan gum, guar gum and or inulin. If you use a flour that does not contain one of these binders, add 1/2 tsp xanthan gum to the recipe.
Apple Pie Filling
Unlike an actual apple pie, the pie filling is added to the cupcakes once they’re baked. The filling is cooked on the stove with sugar and spices and a little bit of thickener.
For the spices, you can use either a pumpkin spice blend or a combination cinnamon, clove and ginger. If you have a preference or dislike for one of the spices, feel free to adjust the amount. I personally love a little extra ginger to add some zing.
Granny Smith apples are one of the best apples for apple pie filling. They’re a great combination of sweet and tart and are firm enough to hold up. Pink Lady and gala apples are good options as well. They are both firm and sweet with a hint of tart.
The sweetness of your apples are will determine how much sugar you add. Start with two tablespoons of sugar. Once the filling is cooked, taste. If it seems a little too tart, add more sugar, 2 teaspoons at a time until you’re satisfied with the flavor.
The recipe makes enough to fill the cupcakes. If you would like to have enough to top the cupcakes as well, double the filling recipe below.
How to Fill Cupcakes
Use either a cupcake corer, a small knife or even an apple corer to cut a 1″ hole in the center of the cupcakes. If using a knife or apple corer, angle it a little towards the middle to avoid cutting through the bottom of the cupcake.
Remove the cut piece and clean any crumbs out, creating a nice wide space for the filling.
Spoon in some filling so that it is level with the top of the cupcakes.
Suggestion for the discard pieces of cupcake: Place the pieces on a sheet pan and bake in the oven for about 20 minutes at 300°F or until they are dry and toasted. Break the pieces up into crumbs and top ice cream or frozen yogurt.
I keep the warm spices and apple flavor continuing into the frosting with an apple spice buttercream. To inject the apple flavor, you’ll simmer some apple juice until it turns into a thick syrup. This way, it will add concentrated flavor without making the frosting runny.
Cinnamon, clove and ginger are also added to the frosting or use a pumpkin spice blend instead.
If you prefer a more neutral frosting, my vanilla buttercream frosting or tangy pipeable cream cheese frosting would both be perfect on these cupcakes.
Gluten-Free Apple Pie Cupcakes
- 1 c + 2 Tbsp gluten-free flour blend** gluten-free, rice-free flour option
- 1¼ tsp baking powder
- ½ tsp ground cinnamon
- ¼ tsp salt
- ¾ c sugar
- 4 Tbsp (½ stick or 2 oz) of unsalted butter, softened to room temp
- ⅓ c oil (avocado, sunflower, canola or other neutral flavored vegetable oil)
- ⅓ c milk or dairy-free milk substitute, room temperature (heat for 10 seconds in the microwave)
- 1 tsp vanilla extract, powder or bean paste
- 2 large eggs, room temperature*
Apple Pie Filling
- 2 medium sized granny smith apples (or other firm apples like pink lady or gala)
- ¼ c water
- 1 Tbsp lemon juice
- 3-4 Tbsp sugar
- ¾ tsp cinnamon
- ⅛ tsp ground ginger
- ⅛ tsp ground cloves
- or replace the 3 spices above with 1 tsp pumpkin spice blend
- 1 tsp corn starch mixed with 1 Tbsp cold water
Apple Spice Buttercream Frosting
- 1½ c apple juice
- 12 Tbsp (1½ sticks/6 oz) soft, unsalted butter
- 2¼ c powdered sugar, sifted
- ½ tsp cinnamon
- ⅛ tsp ground ginger
- 2 pinches ground cloves
- or replace the 3 spices above with ¾ tsp pumpkin spice blend
- ½ tsp vanilla extract, powder or bean paste
Make the Cupcakes
- Preheat the oven to 350°F. Line a cupcake pan with paper liners.
- NOTE: Because this recipe includes soft butter, it is very important that the eggs and milk are at room temp. Place cold eggs in a bowl of warm water to take the chill off and heat the milk in the microwave for 10-15 seconds.
- In a small mixing bowl, combine the flour, baking powder, cinnamon and salt.
- In a medium sized bowl or the bowl of a stand mixer, cream the butter and sugar beating on high for about 30 seconds and scraping down the bowl a few times,
- Add the room temp milk, oil and vanilla and beat on medium high speed until combined. Scrape down the sides and bottom of the bowl.
- Add the room temp eggs and beat on medium speed until smooth.
- Add the dry ingredients and mix on medium-low for 5 seconds. Scrape down the sides and bottom of the bowl and beat until smooth.
- Divide the batter evenly among the cupcake liners (about 2 heaping tablespoons each).
- Bake 18-20 minutes or until the tops are set and bounce back from a gentle tap. While the cupcakes are baking and cooling make the filling and frosting.
- Cool the cupcakes in the pan for 5 minutes, then transfer to a wire rack to cool completely.
Make the Apple Pie Filling
- This makes enough to fill the cupcakes. If you want to add a little filling on top of the frosting, double the recipe.
- Place the lemon juice into a 2 quart (medium sized) pot.
- Peel, core and dice the apples into ¼ inch chunks. The chunks need to be small to make it work in a cupcake. As you chop, transfer the diced apple to the pot with lemon juice and toss to prevent browning.
- Add the water and sugar to the pot and place it over medium heat on the stove top.
- Stir in the sugar and spices.
- Cook over medium heat, stirring occasionally, for 10-15 minutes or until the apples are softened but not mushy.
- Add the corn starch/water mixture, stirring constantly until the liquid thickens. If it gets too thick, stir in a tablespoon or 2 of water to thin it out.
- Transfer the filling to a bowl to cool.
Make the Frosting
- Place the apple juice into a large pot and place over medium high heat on the stove.
- Simmer for 10-15 minutes or until the juice is syrupy and reduced to just 2 tablespoons of liquid. Place the reduction into a bowl to cool.
- In a large mixing bowl or the bowl of a stand mixer, beat the butter on high for 1 minute.
- Add half of the sifted powdered sugar and beat on low-medium for 15 seconds.
- Add the remaining powdered sugar and the spices and beat on medium-low for 15 seconds. Scrape down the sides and bottom of the bowl and beat on medium-high for another 10 seconds.
- Add the vanilla and apple reduction and beat another 15 seconds. Overbeating will create air pockets in the frosting.
Assemble the Cupcakes
- Do not try to core the cupcakes until they are completely cooled. Use a cupcake corer or a small knife to cut a 1" hole in the center of the cupcakes. DO NOT go all the way to the bottom
- Remove the cut piece and clean any crumbs out, creating a nice wide space for the filling.
- Spoon in some filling so that it is level with the top of the cupcakes.
- Top with frosting.
- These cupcakes can stay at room temperature for 2 days, then refrigerate.
Amazing gluten-free-apple cup cake. I made it last night and everbody love it. They could not believe that were glute free.
Thanks for the recipe.
Janet Harlow says
Thank you so much! I am so happy that you enjoyed them as much as I do!