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Gluten Free Spice Cupcakes

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A small batch of Gluten Free Spice Cupcakes made with an almond flour blend and full of cozy spices.  The cupcakes are tender and moist and finished with a Apple Spice Cream Cheese Frosting for a harmonious blend of holiday flavors.

Gluten free spice cupcakes arranged on parchment paper

Gluten Free Spice Cupcakes

You almost have to have a Spice Cupcake recipe for your Fall and Winter baking!  At least, I think you do.  Because there may be a time when you are overwhelmed with all of the Pumpkin Spice recipes, or everything being highlighted with Peppermint.  Not that they are bad (pretty yummy as a matter of fact), but it is nice to have a little flavor variety in your baking repertoire.

This Gluten Free Spice Cupcake recipe was adapted from the Vanilla Gluten Free Cupcake recipe already on the blog.  It is made with my almond flour (and Paleo!) blend and it produces a cupcake that you’d be hard pressed to tell it was gluten free!  The cupcakes have all of the same delicious qualities  you love in a traditional cupcake:

  • Moist – There is that ‘M’ word, but I will proudly continue to use it when it comes to describing a baked good.  Because let’s face it, you probably want to know that the cupcake isn’t actually dry, right?!
  • Soft – These Gluten Free Spice Cupcakes are also soft and tender.  I find some gluten free baking can yield a pretty dense and heavy bake, but not these cupcakes!
  • Easy – You don’t even need to break out the hand mixer for these cupcakes.  Well, except for the frosting.   
  • Flavor Bomb – It is hard not to have a lot of flavor in the cupcakes when they feature molasses, brown sugar, AND all of the warm spices.
  • Versatile – Not only can you add (or subtract) some of the spices, but you can also bake the batter into a single layer 6-inch cake.  Perfect for snacking!

Small Batch Cupcakes That Are Also Gluten Free

Did I mention that these Gluten Free Spice Cupcakes are also small batch?!  I figure the gluten free recipes on the blog needed a small batch cupcake added to the list.  The recipe yields 4 cupcakes – making a great portion for smaller crowds.  Or if you want to try a variety of bakes, but don’t want to make dozens!

Single gluten free spice cupcake with frosting on a wooden plate

What You Need To Make Gluten Free Spice Cupcakes


See below for a little more detail about the Paleo Almond Flour blend I use for the Gluten Free Spice Cupcakes

  • Almond Flour – Blanched almond flour is what I use and I have provided a link in the recipe.
  • Arrowroot Flour – You may see arrowroot flour or arrowroot starch, depending on the brand.  They are the same thing.
  • Coconut Flour
  • Tapioca Flour – Same as the Arrowroot, you may see tapioca flour or tapioca starch and they are the same.
  • Baking Powder and Baking Soda – To keep the cupcakes 100 percent gluten free, check the label on the baking powder.  Some brands may use a wheat based starch in the baking powder.
  • Cinnamon, Allspice, Nutmeg, Ginger, and Cloves – All of these spices is what makes the cupcakes Spice Cupcakes!
  • Salt
  • Egg
  • Milk – I use unsweetened coconut milk, and any milk will work.
  • Molasses – My preferences is unsulphured molasses for the lighter, yet sweet flavor.
  • Dark Brown Sugar – The dark brown sugar compliments the molasses and adds a little moisture.
  • Coconut Oil – Coconut oil acts as the fat in the cupcakes – much like butter would.
  • Vanilla Extract
  • Cream Cheese – I prefer to use full-fat cream cheese for frostings because of the flavor and consistency.
  • Heavy Cream
  • Freeze Dried Apples – The freeze dried apples give the frosting a bright flavor without adding unnecessary moisture.

Baking Equipment

  • Muffin/Cupcake Pan with Liners
  • Mixing Bowls
  • Small Food Processor or Blender – To grind the freeze dried apples to powder.
  • Hand Held Mixer

*Paleo/Almond Flour Blend

  • Blanched Almond Flour
    • The base in the flour blend.  Almond flour produces a light and fluffy cake-like bake.  Which makes it a great option for cakes, cupcakes, muffins, and even gluten free cookies.  I will always recommend a blanched, super-fine almond flour.  This means the flour is ground as fine as it can be (before turning into butter), and the skins are removed.
  • Arrowroot Starch/Flour
    • Flour and starch are used interchangeably in the package titles.  Arrowroot aids in the tender texture we like in baked goods.  It also adds structure to the crumb.  
  • Coconut Flour
    • Ground from dried coconut meat, coconut flour is super absorbent.  It should be blended with other flours as it does not work well as a 1:1 swap.  Its absorbency allows swapping granulated sugar for liquid sweeteners –  like maple syrup or honey.  I also find it counter-balances other wet ingredients in the recipe.
  • Tapioca Starch/Flour
    • Another where flour and starch are used interchangeably in package titles.  Tapioca adds a little more chew to the baked good – where normally we’d get that from gluten in all-purpose flour.  And I have found in baked goods, it gives a ‘crisp’ exterior.

Tips For Making Gluten Free Spice Cupcakes 

  • Blanched, superfine almond flour is my recommendation – The blanched almond flour means the skins of the almonds have been removed before the almonds have been ground to flour.  I prefer blanched because I don’t want any extra texture in the flour.
  • Use unsulpurhed molasses – Unsulphured molasses doesn’t have a overly strong flavor, like Blackstrap Molasses.  And since we are not making molasses cupcakes, we don’t want the flavor to overpower the spices.
  • Dark brown sugar adds extra flavor – Though, if all you have on hand is light brown sugar, that will work too!
  • Add a tiny pinch of extra cloves for extra spice – A little ground clove goes a long way.  But if you prefer an extra ‘spicy’ Spice Cupcake, you can add a tiny bit extra.  And I mean tiny.  Otherwise your cupcakes may leave your mouth numb!
  • Cool the cupcakes completely – Gluten free baked goods just taste better when they have had the chance to cool completely.  Additionally, you want cool cupcakes before your frost them!
  • Make the frosting first – This isn’t necessary, but the frosting will set up a little more if it has some time in the refrigerator.
Row of frosted gluten free spice cupcakes

Common Questions For Making Gluten Free Spice Cupcakes

Can this recipe be doubled?

I have not tested doubling the recipe, but you could certainly try it. Let me know how it turns out!

Can I make this into a small cake instead of cupcakes?

Yes! It will make a small, single layer 6-inch cake. I recommend a 6-inch round cake pan.

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

I prefer the paleo flour blend because I think it produces a more moist cupcake. With that, I don’t bake with the 1:1 flour blends because I find them dry. You can certainly try to substitute and let me know how it turns out!

Can I substitute ingredients to make the cupcakes vegan as well?

The only swap you would need is the egg, and you can certainly find guidance on how to swap an egg with a flax egg or even applesauce. I have not tried either.

I’d like to use a sugar alternative. Will that work?

You can certainly try it, though I can’t provide any guidance on proper substitutions as I don’t work with sugar alternatives! I do however, have a Gluten Free Vanilla Cupcake recipe on the blog that uses maple syrup as the sweetener, if you want to try that and add in some of the spices.

Where do I find freeze dried apples for the frosting?

Most groceries should have them in the aisle with the nuts and fruits. I purchase mine at Target, but if you are having a hard time finding them, Amazon is always a great resource.

How should I store leftover cupcakes?

If you have any(!), the leftovers can be stored covered in the refrigerator. I recommend the fridge because of the cream cheese in the frosting.

Small batch of spice cupcakes arranged on a wooden platter

More Gluten Free Dessert Recipes

Frosted gluten free spice cupcakes on small wooden plates

Gluten Free Spice Cupcakes

Yield: 4 Cupcakes
A small batch of Gluten Free Spice Cupcakes made with an almond flour blend and full of cozy spices.  The cupcakes are tender and moist and finished with a Apple Spice Cream Cheese Frosting for a harmonious blend of holiday flavors.
Prep10 minutes
Cook22 minutes
Total32 minutes


  • 1 – Muffin/Cupcake Pan


Vanilla Cupcakes

Apple Spice Cream Cheese Frosting


Spice Cupcakes

  • Preheat the oven to 350F degrees and adjust the oven rack to the middle position. Line the muffin/cupcake pan with 4 cupcake liners.
  • In a medium bowl, add the egg, milk, molasses, brown sugar, melted coconut oil, and vanilla extract. Whisk until fully incorporated.
  • In a small mixing bowl, whisk together the almond flour, arrowroot flour, coconut flour, tapioca flour, baking powder, baking soda, salt, and spices.
  • Sprinkle the dry ingredients over the wet ingredients and whisk until combined and no dry streaks remain.
  • Pour the cupcake batter equally into the prepared pan with liners. Bake the cupcakes for 20 to 22 minutes, or until the cupcakes are springy to the touch and a toothpick inserted in the middle comes out clean. 
  • Cool the cupcakes in the pan set on a wire cooling rack for 5 minutes. Then transfer the cupcakes to the wire rack to cool completely before frosting.

Apple Spice Cream Cheese Frosting

  • In a small blender or food processor, pulse the freeze dried apples to a fine powder. It may take half of a 1.25 ounce bag to get the amount needed for the frosting.
  • In a medium mixing bowl, add the cream cheese and heavy cream. Use a hand held mixer on medium speed to beat until smooth and creamy. Sprinkle in the apple powder, cinnamon, and powdered sugar. Beat on low speed to incorporate, then turn up to medium until and beat until the frosting is thick and fluffy. Note – Add more powdered sugar if you prefer a thicker frosting, and more apple powder if you prefer a stronger apple flavor.
  • The frosting is ready to use right away, or can be covered and refrigerated until ready to use.
  • Pipe or spread the frosting onto cooled cupcakes, top with festive sprinkles (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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