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Gluten Free Apple Spice Cupcakes

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This small batch recipe for Gluten Free Apple Spice Cupcakes is adapted from my spice cupcakes, and include plenty of apple pie spices and fresh apple chunks.  The cupcakes are perfectly soft, moist, and make the ideal fall cupcake when finished with dairy free caramel frosting!

A single gluten free apple cupcake with frosting on a small wood coaster.

Apple Spice Cupcakes Recipe

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!

And while it may seem appropriate to start sharing a bunch of pumpkin recipes, I’m adding to my apple lineup with these Gluten Free Apple Spice Cupcakes.  A good gluten free cupcake bejeweled with apples is a fall must have, in my book.

Here’s what you can expect with these small batch gluten free apple spice 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 you apple.  🙂
  • Made with an almond flour blend – The majority of my gluten free 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 cookies?!
A cake platter of frosted gluten free apple spice cupcakes on a table.

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 loose 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!

Diced apples in a small glass bowl.

What You’ll Need To Make These Gluten Free Fall Flavored Cupcakes

dry 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 loaf and cinnamon swirl 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.  The difference is my version uses ginger and cardamom.  Store bought may use allspice and nutmeg instead.  However, I think it is completely user preference when it comes to spices!

Wet Ingredients

  • Organic Cane Sugar – I’m using a granulated sugar in this recipe purely to yield a soft cake-like texture.  Therefore, I am recommending organic cane sugar because it is not as processed as white sugar.  
  • 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!

Baking Equipment

  • Cupcake Pan with Cupcake Liners
  • Mixing Bowls

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.  Or to keep things traditional, vanilla or chocolate frosting would still give off fall vibes!

But, if you need a little more inspiration, check out the frosting and cupcake recipes on the blog for a few more frosting ideas!

Fluffy caramel frosting made without butter on a whisk.

Success Tips For Making Gluten Free apple Cupcakes

  • Peeling the apple is optional – There are recipes where I don’t peel the apples, and others that I do.  It is totally 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.
  • Use room temperature liquid ingredients – When all the ingredients start out at the same temperature, they will mix easier and bake more consistently.
  • 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.
  • Bake until the recommended time – The cupcakes may look done a few minutes earlier than noted in the recipe.  However, gluten free baking does require extra bake time!  Keep the cupcakes in the oven until time is up to make sure they get baked all the way through!
  • 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!
A single apple spice gluten free cupcake with the cupcake liner removed on a small cupcake stand.
Caramel butter free frosting piped onto a cupcake sitting on a small cupcake stand.

FAQ’s: small batch Gluten Free Apple Spice Cupcakes

Can this recipe be doubled?

I haven’t tested a larger batch, but if you do, please let me know how they turn out!

Will a 1:1 gluten free flour blend work instead of the almond flour blend?

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.

Can I make the cupcakes into a cake instead?

This recipe will work to make a single layer 6-inch cake.

I’d like to use a refined sugar instead. What another sweetener will work?

I haven’t tested this recipe with a liquid sweetener like maple syrup or honey. It may work. The cupcakes may just turn out more like muffins (a little more dense).

How should I store leftover cupcakes?

If there are any (!), the cupcakes can be stored at room temperature for up to 3 days. Note, 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!

Two frosted apple spice gluten free cupcakes on a wood tray.

Gluten Free Apple Spice Cucpakes

Yield: 4 Cupcakes
This small batch recipe for Gluten Free Apple Spice Cupcakes is adapted from my spice cupcakes, and include plenty of apple pie spices and fresh apple chunks.  The cupcakes are perfectly soft, moist, and make the ideal fall cupcake when finished with dairy free caramel frosting!
Prep20 minutes
Cook24 minutes
Total44 minutes


  • 1 – Muffin/Cupcake Pan



  • 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.
  • 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.
  • 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.
  • 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.
  • Frosting – Prepare the Caramel Dairy Free Frosting while the cupcakes are baking and cooling. Or you can use any frosting you prefer.
  • Frost completely cool cupcakes, top with an apple slice garnish (optional), and Enjoy!
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Course: Dessert
Cuisine: American
Author: Erin Cernich
Nutrition information is calculated by a third-party and should only be considered an estimate and not a guarantee.
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about the author ...

I'm Erin and I'm all about desserts - and a little bit of butter!

I've tested, written, and photographed hundreds of recipes on my website. Here you'll find the tastiest small batch gluten free and traditional desserts - all homemade, all simple, and all for you!

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