This small batch recipe for Gluten Free Apple Spice Cupcakes is adapted from my spice small batch cupcakes, and includes plenty of apple pie spices and fresh apple chunks. The cupcakes are perfectly soft, and moist, and make the ideal fall cupcake when finished with dairy-free caramel frosting!
Gluten Free Apple Spice Cupcakes
I think it is safe to say that fall baking is upon us! Food Network is starting to air my favorite fall tv shows, I’ve officially turned off the AC, and I can open the windows at night to enjoy the crisp cool air. Needless to say, I’m a happy girl!
While it may seem appropriate to start sharing a bunch of small batch pumpkin recipes, I’m adding to my small batch apple desserts lineup with these gluten free apple cupcakes. A good gluten free cupcake bejeweled with apples is a fall must have, in my book.
Why You’ll Love These Cupcakes
- Easy – Two bowls, no mixers, and a whisk is all you need! Oh, and if you count the knife and cutting board to prepare your apple. 🙂
- Made with an almond flour blend – The majority of my gluten free small batch recipes use an almond flour blend to yield tender and moist bakes.
- Full of cozy, fall spices – Spices like cinnamon, ginger, and my all-time favorite – cardamom!
- Fresh apple chunks in every bite – When you tout an apple cupcake, you better get an apple in each bite! The small chunks make this possible without weighing down the cupcakes.
- Ideal for smaller gatherings – Or if you want to prepare a variety of fall desserts. Since you already have the apple, how about some soft caramel apple small batch cookies?!

What Type Of Apple Is Best For Baking?
Oh, this question. You will find many opinions out there, but I usually recommend using any apple that you would like to eat. This of course comes with a disclaimer: do not select an apple that is too soft like a Red Delicious or Gala apple. They can lose their flavor when baked and will get too soft when baked.
I tend to stick to a firmer apple that is still sweet, like a Honeycrisp. Plus, these are the apples I grab when I just want to eat one!

Ingredients
- Fresh Apple – I used a Honeycrisp, but a Pink Lady or Braeburn will work. And of course, a Granny Smith with work as well.
- Almond Flour – The base flour and yields a soft, fluffy, cake.
- Arrowroot Flour – Depending on the brand, arrowroot may also be called a starch. They are the same thing.
- Coconut Flour – Coconut flour is very absorbent and I find it aids in the texture of gluten free bakes and helps the cupcakes not get too moist.
- Sweet Rice Flour – I use sweet rice flour to give the cupcakes a soft texture. Similar to my chocolate chip mini gluten free loaf and maple cinnamon swirl mini gluten free bread.
- Baking Powder, Baking Soda, and Salt – Leaveners, texture, and flavor.
- Cinnamon, Ginger, and Cardamom – My version of apple pie spice. But you can certainly use store bought pre-made apple pie spice if you prefer.
- Organic Cane Sugar – Or regular granulated white sugar will work. I like organic cane sugar for its flavor.
- Coconut Oil – Coconut oil is a (healthier) substitute for butter or canola oil.
- Egg – 1 large egg is all we need.
- Milk – I use unsweetened So Delicious coconut milk, but any milk will work.
- Apple Cider Vinegar – The apple cider vinegar helps make the cupcakes tender, plus it acts with the baking soda the give the cupcakes a little more help on rising. I find gluten free baking needs a little extra help with leavening.
- Vanilla Extract – Flavor!


What Flavors Of Frosting Go Well On Apple Cupcakes?
It may be cliché, but I always think of caramel apple when fall rolls around. And while I may be partial to caramel, an apple spice cream cheese frosting would be delicious.
But, if you need a little more inspiration, check out the small batch frosting recipes for a few more frosting ideas!

Helpful Tips
- Peeling the apple is optional – There are recipes where I don’t peel the apples and others that I do. It is a personal preference.
- Cut the apples into small chunks – The cupcakes are small, and we want small chunks to get into every bite! I would say about 1/4-inch chunks
- Whisk the flours together well – I find that some of the gluten free flours – especially almond flour – like to clump. I recommend breaking up the clumps with your fingers or the whisk to avoid clumps in the final bake.
- Let the batter rest for 5 minutes before baking – I find that bakes that use sweet rice flour benefit from a few minutes of rest time to allow the batter to hydrate and bake more evenly.
- Cool completely – It may be tempting to dive right in, but I find gluten free bakes taste better when they are completely cool. Additionally, you don’t want to frost warm cupcakes – the frosting will melt!


Recipe FAQ
I can’t say for certain. I find the 1:1 blends to be much drier than my blend and the results may be different.
This recipe will work to make a single-layer 6-inch cake.
If there are any (!), the cupcakes can be stored at room temperature for up to 3 days. They may seem extra moist after the first day. That is the moisture from the almond flour coming through. This is ok, and they still taste delicious!

Gluten Free Apple Spice Cucpakes
EQUIPMENT
INGREDIENTS
- ¼ cup blanched almond flour
- 2 tablespoons arrowroot flour
- 1 tablespoon coconut flour
- 1 tablespoon sweet white rice flour
- ¼ teaspoon baking powder
- ⅛ teaspoon baking soda
- ½ teaspoon ground cinnamon
- ½ teaspoon ground ginger
- ¼ teaspoon ground cardamom
- ⅛ teaspoon salt
- ¼ cup organic cane sugar (or any granulated sugar)
- 2 tablespoons cold pressed refined coconut oil, melted
- 1 large egg (room temperature)
- 2 tablespoons milk
- ¼ teaspoon apple cider vinegar (or white distilled vinegar)
- ¾ teaspoon vanilla extract
- ⅓ cup apple, peeled and chopped into small chunks (about 1/4 of 1 large apple)
INSTRUCTIONS
- Preheat oven to 325F degrees and adjust the oven rack to the middle position. Line a cupcake pan with 4 cupcake liners.
- Peel the apple and chop about 1/4 of the apple into small chunks.
- In a small mixing bowl, whisk together the almond, arrowroot, coconut, and sweet rice flour. Break up any flour clumps with your finger or the whisk. Add the baking powder, baking soda, salt, and spices. Whisk until well combined. Note – You can substitute the spices for pre-made store bought apple pie spice if you prefer.1/4 cup blanched almond flour, 2 tablespoons arrowroot flour, 1 tablespoon coconut flour, 1 tablespoon sweet white rice flour, 1/4 teaspoon baking powder, 1/8 teaspoon baking soda, 1/2 teaspoon ground cinnamon, 1/2 teaspoon ground ginger, 1/4 teaspoon ground cardamom, 1/8 teaspoon salt
- In a medium mixing bowl, add the sugar and coconut oil. Whisk to combine. Add the egg, vanilla extract, milk and vinegar. Whisk to combine until smooth and the egg has been fully incorporated.1/4 cup organic cane sugar, 2 tablespoons cold pressed refined coconut oil, melted, 1 large egg, 2 tablespoons milk, 1/4 teaspoon apple cider vinegar, 3/4 teaspoon vanilla extract
- Sprinkle the dry ingredients over the wet and whisk to combine and no dry streaks remain. Then, add the apples and stir until just combined.1/3 cup apple, peeled and chopped into small chunks
- Pour the batter equally into the cupcake liners. Tip – Use a cookie scoop to get equal portions, and less mess!
- Bake for 22 to 24 minutes, or until the cupcakes are springy to the touch and a toothpick inserted in the middle comes out mostly clean.
- Cool the cupcakes in the pan set on a wire cooling rack for 10 minutes. Transfer the cupcakes to the rack to cool completely.
- These cupcakes are delicious with my caramel dairy free frosting or my cinnamon maple cream cheese frosting!
- Frost completely cool cupcakes, top with an apple slice garnish, and Enjoy!
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about the author ...
With years of experience baking for two in my own small household, I know about the love for desserts without the leftovers! I’ve tested, written, and photographed the hundreds of small batch dessert recipes on my website. From traditional to gluten free desserts for two, I have the recipe for you!