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Whole Wheat Chocolate Cupcakes

Whole Wheat Chocolate Cupcakes

I admit it, I am a cupcake junkie!! And…I love chocolate!!  Of course, since today is National Chocolate Cupcake Day, I felt it necessary to show my love for these creations by creating whole wheat chocolate cupcakes.

There’s just something about tiny decorated little cakes that I truly enjoy.  I set out on a journey with this post to see if it was possible to make some healthy adjustments to a “typical” cake recipe with favorable results.

My goal: to see if a “healthier” whole wheat cupcake would maintain the delicate, moist texture you expect in a good cupcake and the creamy sweetness of its frosting.

The biggest question I pondered as I started this process is that maybe it’s just best to leave thing alone.  And that maybe, rather than trying to put a healthy spin on such a yummy dessert, it was best to simply enjoy it in its original form.

NOTE:  This post includes affiliate links which means that if you click through and purchase, I do receive some small financial benefit which helps me to continue to provide you with free content.    

The recent cupcake craze

Cupcake ATM in NYC

In the last several years, cupcakes really hit the scene as a trend.  I lived in New York City during this recent cupcake craze.  During this time, it seemed like every time I turned around a new place was popping up offering their spin on cupcakes.  Some of the more iconic places include Magnolia Bakery, which received recognition when it appeared on the HBO series, Sex in the City.  And yes, they have a pretty good cupcake.

Then there was Sprinkles, another NYC cupcake giant, which actually installed a cupcake ATM on Lexington Avenue in Manhattan.  You made your selections, paid by credit card and out came a lovely little box with your cupcake inside.   A fairly decent cupcake, but also a very clever idea!!  Then there was the place with adorable tiny cupcakes.  You could mix and match your order from a variety of flavors and looks in teeny tiny versions.  

Getting cupcake box from cupcake ATM in NYC.

Cupcake Basics

The first mention of a cupcake in a U.S. recipe/cook book goes all the way back to the early 1800’s.  So they’ve been around for a while. 

Any cake recipe can easily be turned into cupcakes instead of a large cake.  You will just need to adjust your timing as they will need less time to cook.  Basic cake ingredients include flour, eggs, milk, butter and sugar.  There are of course other flavoring and leavening agents that go into a cake, but the above contribute the basic nutritional content of the cupcake.

My all-time favorite cake/cupcake combination is chocolate cake with a simple white frosting.  No joke – I LOVE it!!!  So, when I ran across a recent “healthy” chocolate cupcake recipe, I decided I needed to try out creating my own version for whole wheat chocolate cupcakes.


The process

I wanted to make two basic changes in the cupcake recipe to improve the nutrition. First, I wanted to find a suitable substitute for the butter and second, I wanted to replace the white flour with whole wheat or other flour to add fiber to the cupcake.

I am going to be completely honest – I am not a great baker.  I don’t have the patience for it.  To be really good and especially when you are developing recipes, it requires patience and accuracy which I do not have.  I started with a recipe that sounded great!!!  It used avocado in place of butter usually found in a cupcake.


Replacing the butter

The primary purpose of butter in baking is to contribute flavor and texture to the baked good. The way butter covers the proteins and starches in the flour creates a delicate texture.

So what’s the big deal about eliminating the butter?  Well, as it is full of saturated fat I felt that one way to create a healthier cupcake was to get find a reasonable replacement.  Avocados naturally have a texture similar to butter, so I thought the avocado would make a suitable substitute for the butter.  But honestly, for me the avocado didn’t work as well as I wanted and created a much denser and heavier cake than I wanted. Next, I tested another version with Greek yogurt instead of butter.  The results were a much better texture.


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Replacing the flour for whole wheat chocolate cupcakes

In the final recipe I used a combination of whole wheat flour and almond flour as the base for the cupcake.

The first batch with the avocado was also made only with whole wheat flour.  In my opinion, the heaviness in this batch came from the flour as well as the avocado.  In the second recipe I added almond flour in combination with the whole wheat flour and I found it resulted in a more delicate cake. 

It is necessary when using these flours to add more liquid to the batter as they absorb more.  I doubled the amount of milk in the recipe to compensate. 

Please note that your batter should be pourable so if it isn’t, you should add more milk to get it to that consistency.


My thoughts on coconut sugar

The first recipe I tested contained coconut sugar in place of regular sugar.  I decided to try it with the coconut sugar to just see how it would come out as I hadn’t really baked with it before.

I did a little research on coconut sugar to see if it truly is a healthier option to regular sugar. 

What I discovered is that coconut sugar is very similar to regular sugar.  They have a similar caloric content, and both are considered an added sugar.

Coconut sugar has a slightly lower glycemic index value than regular sugar (54 instead of 60 in regular sugar).  Glycemic index is a measure of how quickly a particular food raises your blood sugar level. 

The only real advantage that I see in using the coconut sugar is that it is often less processed than regular sugar. 

I didn’t see any major differences in the outcome of the final product.  Another thing to note is that coconut sugar is higher in cost than regular sugar and so at the end, my opinion is to stick with regular granulated sugar.

The best frosting for whole wheat chocolate cupcakes

Closeup of a whole wheat chocolate cupcake.

No cupcake is complete without frosting.  And this is where I found the biggest problem in creating my recipe for whole wheat chocolate cupcakes.

A basic vanilla buttercream frosting is a combination of butter and sugar.  My first attempt using Greek yogurt as a replacement for the butter, but the consistency wasn’t right.  

Next, I tried the same combination and added a bit of mascarpone cheese (you could also use cream cheese) to thicken it up.  There wasn’t anything really wrong with it, it was sweet and creamy, but it had too much of a “milk” flavor for me to get super excited about it.

In the end, I found the frosting too difficult to change and still yield in results that I was content with, so I settled on using a basic whipped cream frosting.  The light and airy texture and gentle sweetness really worked well with this cupcake recipe.  

The recipe

Delicious whole wheat chocolate cupcakes are frosted and ready to eat!

Whole Wheat Chocolate Cupcakes with Whipped Cream Frosting

Rich and delicious chocolate cupcakes with extra fiber and protein topped with light creamy white frosting.
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Course: Dessert, Snack
Cuisine: American
Keyword: cupcakes, kid friendly, whipped cream, whole grains
Prep Time: 10 minutes
Cook Time: 20 minutes
Total Time: 30 minutes
Servings: 12 people
Author: Lyn Croyle



  • 1/4 cup Greek yogurt
  • 1 cup coconut sugar
  • 2 large eggs
  • 2 T olive oil
  • 1 3/4 cup whole wheat flour
  • 1 cup almond flour
  • 1/2 cup unsweetened cocoa powder
  • 1 teaspoon baking soda
  • 1/4 teaspoon baking powder
  • 1/4 teaspoon salt
  • 1 cup almond milk
  • 1/2 teaspoon vanilla extract
  • 1/2 cup hot coffee


  • 1 ½ cup whipping cream
  • 2 T granulated white sugar
  • 3/4 tsp vanilla extract



  • Preheat oven to 350 degrees.
  • Sift all the dry ingredients into a separate bowl, flour, cocoa, baking soda, baking powder and salt. Whisk to blend and set aside.
  • In the mixing bowl, beat together the yogurt and sugar until mixed thoroughly. Add the egg one at a time and mix well following each. Add the oil and vanilla. You may need to scrape down the sides and bottom of the bowl during the mixing process to incorporate all the ingredients.
  • Mixing on medium speed, alternately add the flour mixture and milk to the sugar mixture, beginning and ending with the dry ingredients.
  • Once the last portion of dry ingredients are added, add the cup of hot coffee. The batter will be very thin. Don't worry this is how it should be.
  • Bake at 350 degrees for 18 to 20 minutes. Allow to cool on a baking rack.


  • Before starting, chill the bowl and whisk in the refrigerator for 20 minutes.
  • Pour the heavy cream into the bowl and mix on medium-high speed until the cream begins to thicken.
  • Slowly add the sugar and continue to beat, soft peaks will begin to form.
  • After all the sugar is added, add the value and continue to whisk by hand until stiff peaks are formed. You will know that stiff peaks have formed when the cream will stand up straight when you pull the whisk straight up and out of the mixture.
  • When the cupcakes are completely cool, add the frosting.


Each cupcake gets about 2 T of frosting.
The frosting needs to stay refrigerated so either wait to frost cupcakes until just before serving or frost ahead and keep cupcakes refrigerated until you are ready to serve.

The results

In the end, I feel like I was pleased with my recipe for whole wheat chocolate cupcakes.  And I would definitely make these again. 

I do have a couple things to note about this recipe.  First, I believe the cupcakes definitely tasted better the first day. I felt like by day two they were firmer and had lost some of the delicateness that was there when they were fresh.

Also, this icing doesn’t hold up for a great length of time so I recommend icing them as close to the serving time as possible.

Lastly, I also realize that there are definitely some sacrifices made when making sweet baked goods healthier.  So I imagine every once in a while I will still likely indulge in a delicious “regular” cupcake and do so with great pleasure.

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Did you try out this recipe?  If so, share your pictures on Instagram and be sure to tag @cookeatlivelove.  

If you have any comments on this recipe or other content you would like to see, please comment here on the blog or send me a message via any social media or the contact me page.  

Also, if you liked this recipe, please don’t forget to give the recipe a rating in the recipe card.

Shop this post

The following includes affiliate links for these recommended products from Amazon.  When you click the link and make a purchase, I make a small commission at no cost to you. This allows me to continue creating and providing free content.

Organic Coconut Sugar

Super Fine Almond Flour

Calphalon 12 cup cupcake pan

Fun cupcake decorating options by Sprinkle Pop

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