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Meal Type ยป Desserts ยป Almond Flour Chocolate Cupcakes

Almond Flour Chocolate Cupcakes

Claire Cary

By

Claire Cary

5 from 14 votes
July 12, 2023
Jump to Recipe

These paleo friendly almond flour cupcakes are rich, moist and made in one bowl! They’re completely gluten free, dairy free and refined sugar free but taste like the most indulgent chocolate cupcake.

almond flour cupcakes on a cake stand with berries

Almond flour never fails to amaze me. It honestly might be my favorite gluten free flour to work with. It keeps baked goods so moist thanks to the fat content and gives a deliciously light and fluffy texture.

Plus, almond flour is both gluten and dairy free so it’s perfect for anyone with food sensitivities. Almond flour is great for baking cakes and cupcakes thanks to it’s ability to both add moisture and structure. These almond flour cupcakes are based loosely off my my popular almond flour cake, but with some substitutions to simplify the recipe and of course make them work as cupcakes!

You’ll need a base of almond flour to provide structure and moisture, plus tapioca starch to help bind things together and give a classic cupcake feel, cocoa for the chocolate, eggs for more binding and lift, then some honey, coconut sugar and canned coconut milk for more moisture.

The texture is identical to that of a refined flour and sugar filled chocolate cupcake, you would truly never know these are made with such good for you ingredients! Try my flourless chocolate cake or almond flour vanilla cake next!

ingredients for the recipe in bowls

Key ingredients

ALMOND FLOUR. These almond flour chocolate cupcakes obviously have a base of almond flour! Be sure to use blanched almond flour and not almond meal for this recipe.

EGGS. Eggs will help bind all ingredients together and provide some structure to these cupcakes.

MILK. We’ll be using canned coconut milk which provides a really luscious texture without the need for too much added oil.

OIL. A bit of oil helps to add more moisture. I usually use refined avocado oil.

COCOA. Cocoa powder will of course make these chocolate cupcakes! You can use dutch processed or regular. Same with my gluten free red velvet cupcakes.

HONEY. Honey adds some natural sweetness. I don’t recommend maple syrup since it’s a bit thinner in texture.

COCONUT SUGAR. To keep these refined sugar free we’ll use coconut sugar to sweeten. You can sub for any other granulated sugar if you prefer.

making the batter in a glass bowl

How to make almond flour chocolate cupcakes

PREP. Preheat the oven to 350 degrees Fahrenheit. Line a muffin tray with 12 liners and set aside.

WHISK WET. In a medium bowl, whisk together all wet ingredients.

When measuring the canned coconut milk, be sure to shake the can really well before measuring so the white part and the more watery part are well combined to create a smooth milk.

Some brands don’t shake easily, so just add to a separate bowl and whisk together before measuring.

WHISK DRY. Add in the dry ingredients, making sure to spoon and level the flour, starch and cocoa powder. Whisk to combine until completely smooth.

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It might seem thick at first, but as the eggs break up it’ll become like a normal cake batter.

BAKE. Add to the lined tray and fill each 2/3 of the way up. Bake for 20-24 minutes, I do 22 in my oven, but test with a toothpick. When a toothpick comes out clean, remove from the oven.

COOL & FROST. Let cool in the tray for about 10 minutes, then carefully remove and transfer to a wire rack to finish cooling.

cupcakes in the tray with liners

Buttercream frosting

I just made a regular chocolate buttercream using real butter, but if you follow a strict paleo diet, you are welcome to use palm oil shortening instead of the butter.

To make the frosting, add the room temperature butter to a bowl or bowl of a stand mixer and beat until creamy. Beat in the cocoa, then the powdered sugar, then the milk and vanilla.

Frost the cupcakes once fully cooled and top with berries and sprinkles if desired. I used these large piping tips to frost!

one chocolate cupcake cut in half to show texture

How to store cupcakes

Once prepared, these almond flour chocolate cupcakes will keep at room temperature for 3 days. I recommend keeping them on a plate covered with a foil, or on a cake stand with the lid on.

You can freeze the cupcakes without the frosting. Allow to cool completely, then transfer to a freezer safe bag and freeze for up to 1 month. Let defrost before frosting and enjoy!

almond flour chocolate cupcakes with frosting and berries on top

Ingredient swaps

Tapioca Starch. I really think tapioca starch works best in these almond flour cupcakes, but you can safely sub for arrowroot if you have that instead.

I don’t recommend corn starch since the proportions will change and you’ll need a slightly different amount.

Canned coconut milk. This ingredient is key for the moisture. I don’t recommend swapping for a regular non-dairy milk from a carton as those are more liquidy and watery.

Coconut sugar. You can use any granulated sugar here (except turbinado, I generally advise against using that for most things) such as light brown or regular white sugar.

I used coconut sugar to keep these refined sugar free, but any granulated sugar will work in its place. However, keep the honey as is since that is key for moisture.

Eggs. Unfortunately, this recipe really needs real eggs for best results. Vegan almond flour recipes can be tricky because the eggs add a lot of structure that you miss out on when you omit gluten.

You are welcome to try an egg replacer, I’d be inclined to use a store bought one over flax eggs or apple sauce. If you need a vegan and gluten free recipe, you can try my vegan chocolate cupcakes instead!

up close image of one almond flour cupcake with a white backdrop

Try these recipes next!

  • Almond Flour Chocolate Chip Cookies
  • Paleo Blueberry Muffins
  • Banana Muffins
  • Almond Flour Peanut Butter Cookie
  • Chocolate Protein Cake

Be sure to follow along on on instagram and subscribe to my email list for more recipes and updates. Leave a comment and rating below if you try this recipe and let us know how it turns out!

5 from 14 votes

Almond Flour Chocolate Cupcakes

by: claire cary

These paleo friendly almond flour cupcakes are rich, moist and made in one bowl! They’re completely gluten free and refined sugar free but taste like the most indulgent chocolate cupcake!
/ /
Prep: 10 minutes mins
Cook: 20 minutes mins
Total: 30 minutes mins
12

Ingredients

Dry

  • 1 ⅓ cup fine blanched almond flour
  • ½ cup tapioca starch
  • ½ cup cocoa powder
  • ½ teaspoon baking soda
  • ¼ teaspoon salt

Wet

  • ¾ cup coconut or brown sugar
  • ¼ cup honey
  • ½ cup full fat canned coconut milk
  • 2 large eggs room temperature
  • ¼ cup oil
  • 1 teaspoon vanilla extract
  • 1 teaspoon apple cider vinegar

Frosting

  • ½ cup butter can sub palm oil shortening if paleo
  • ½ cup cocoa powder
  • 2-3 cups powdered sugar or paleo friendly replacement
  • 2-3 tablespoons milk dairy or non-dairy
  • 1 teaspoon vanilla
  • pinch of salt
US Customary – Metric

Instructions

  • Preheat the oven to 350 degrees Fahrenheit.
  • Line a muffin tray with 12 liners and set aside.
  • In a medium bowl, whisk together all wet ingredients. It helps to measure the oil first, then the honey in the same 1/4 measuring cup.
  • The honey will slide right out thanks to the oil! When measuring the canned coconut milk, be sure to shake the can really well before measuring so the white part and the more watery part are well combined to create a smooth milk.
  • Some brands don’t shake easily, so just add to a separate bowl and whisk together before measuring if needed or add to a blender.
  • Add in the dry ingredients, making sure to spoon and level the flour, starch and cocoa powder. Whisk to combine until completely smooth. It might seem thick at first, but as the eggs break up it’ll become like a normal cake batter.
  • Add to the lined tray and fill each 2/3 of the way up.
  • Bake for 20-24 minutes, I do 21 in my oven, but test with a toothpick. When a toothpick comes out clean, remove from the oven.
  • Let cool in the tray for about 10 minutes, then carefully remove and transfer to a wire rack to finish cooling.
  • To make the frosting, add the room temperature butter to a bowl or bowl of a stand mixer and beat until creamy. Beat in the cocoa, then the powdered sugar, then the milk and vanilla.
  • Frost the cupcakes once fully cooled (I use these large piping tips) and top with berries and sprinkles if desired.

Notes

Tapioca starch works best here, but you can sub arrowroot instead if that’s what you have!
Honey is preferable to maple syrup, but maple syrup can be used instead if that’s all you have!
Serving: 1cupcake, with frosting / Calories: 323kcal / Carbohydrates: 46g / Protein: 5g / Fat: 20g / Fiber: 4g / Sugar: 29g

Did you make this?

Mention @eatwithclarity or tag #eatwithclarity!

Related posts:

  1. Vegan Chocolate Mug Cake
  2. Almond Flour Vanilla Cake
  3. Almond Flour Blondies
  4. Almond Flour Chocolate Cookies
5 from 14 votes (5 ratings without comment)

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Comments

  1. sandra
    August 24, 2025

    The cupcakes were delicious but wondering if I made into a 9×13 what the time to cook would be? THX5 stars

    Reply
    1. Claire Cary
      August 25, 2025

      There won’t be enough batter for a 9×13 cake, I would suggest making my almond flour chocolate cake and bake in a 9×13. I’d start with about 35 minutes and adjust from there.

      Reply
  2. Tiffany
    August 20, 2025

    Can I use phyllum husk instead of tapioca starch?

    Reply
    1. Claire Cary
      August 21, 2025

      No, but you can try arrowroot starch or cornstarch!

      Reply
  3. Francesca
    January 14, 2025

    Hi, I was wondering if I could replace the canned coconut milk and use instead almond milk?

    Reply
    1. Claire Cary
      January 14, 2025

      I highly recommend sticking with the canned coconut milk as the high fat content adds a lot of moisture to the recipe. If you’re in a pinch, almond milk should be ok.

      Reply
  4. Monica
    December 16, 2024

    I made these chocolate cupcakes to belatedly celebrate our 9 month anniversary because they were reminiscent of our wedding cake. They were moist, light, and decadent. I made a raspberry coconut oil frosting and the sharp contrast of the raspberries with the rich chocolate was perfect. Absolutely the best almond flour recipe I’ve ever tried!5 stars

    Reply
    1. Claire Cary
      December 16, 2024

      Perfect! Thank so much, Monica!

      Reply
  5. Dawn
    April 21, 2024

    Decided to make these for my birthday. GF for 12 years now, and don’t recall in what decade I last had a birthday cake. They were amazing! Everyone loved them. Beautiful soft crumb. Great mouth-feel. Taste perfection. My hub said that was the best cupcake he’s Ever had. Thank you for giving us such a treat.
    I didn’t have enough honey, so used maple syrup. Used coconut oil. GF and DF – Great recipe.5 stars

    Reply
    1. Claire Cary
      April 22, 2024

      Amazing! So glad you loved these, happy birthday!

      Reply
  6. Billy
    January 13, 2024

    Hi, can I substitute the honey with added sugar /sugar substitute?

    Reply
    1. Claire Cary
      January 14, 2024

      I recommend sticking with a liquid sweetener. So either honey or maple syrup for that part!

      Reply
  7. Sunanda
    September 22, 2022

    Is it absolutely needed to use apple cider vinegar as I donโ€™t have it on hand and would prefer not to buy just for the recipe. Can I use lemon or lime juice or any other alternative? Or is it ok to exclude it completely?5 stars

    Reply
    1. Claire Cary
      September 22, 2022

      You need something acidic to activate the baking soda, but lemon is totally fine!

      Reply
  8. Lindsay
    August 12, 2022

    Just made these and they were delicious! They were moist and fluffy and enjoyed by everyone. The frosting came out very sweet and I used sweetened cocoa powder and did not add the coconut sugar. Does the coco powder make a difference? Thanks!5 stars

    Reply
    1. Claire Cary
      August 14, 2022

      I wouldn’t recommend using sweetened cocoa powder! That will definitely make them too sweet.

      Reply
  9. Victoria
    August 9, 2022

    My batter came out to a brownie consistency, couldnโ€™t find my almond flour so I used Cassava flour. But came out really nice! Dense cake only used 1 cup powdered sugar but added a tablespoon or so of Stevia help sweeten the frosting.5 stars

    Reply
    1. Claire Cary
      August 11, 2022

      Was probably more dense because of the flour change, but happy you enjoyed these!

      Reply
  10. Elaina
    November 18, 2021

    Hi! These look amazing! Just wondering if you know if monk fruit sweetener would work instead of coconut sugar? I have a ton on hand, but havenโ€™t worked with it yet in baking. Thanks!5 stars

    Reply
    1. Claire Cary
      November 18, 2021

      I haven’t tried that but it should be ok!

      Reply
  11. Ashley N Barry
    October 15, 2021

    Is there a good substitute for the almond flour? I’m baking for someone with gluten and nut intolerance.

    Reply
    1. Claire Cary
      October 16, 2021

      I would suggest my regular gluten free chocolate cupcakes instead!

      Reply
  12. Karen
    March 28, 2021

    I love this recipe! do you think you could give me a different heathy chocolate frosting recipe?5 stars

    Reply
    1. Claire Cary
      March 28, 2021

      So happy you enjoyed it! I haven’t tried this one from Detoxinista myself, but I trust her and her recipes so I’m sure it would be great! I just don’t currently have my own healthy chocolate frosting on the blog ๐Ÿ™‚ let me know if you try it!

      Reply
  13. Ashlyn
    March 9, 2021

    I made these exactly as the recipe called and they turned out PERFECT! Moist cupcakes and fluffy frosting! I used coconut oil and coconut sugar and usually those have a pretty distinct taste, but you couldn’t taste them at all in the cupcakes themselves!5 stars

    Reply
    1. Claire Cary
      March 9, 2021

      Perfect! So glad you enjoyed them. Refined coconut oil is the way to go if you want to avoid the coconut taste ๐Ÿ™‚

      Reply
claire cary

Welcome,
I’m Claire

Eat With Clarity is a place for gluten free recipes that are just as good as the real thing. With plenty of vegan, vegetarian and paleo options, there is something here for everyone!


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