Whole Wheat Chocolate Cupcakes with Cream Cheese Icing - Pretty Little Apron (2024)

by Dana

When the words “whole wheat chocolate cupcakes” come out of my mouth you are probably envisioning a dry, cardboard-like cupcake that was better left un-eaten. SO not the case here people! I would never suggest a dessert recipe that myfamily hasn’t thoroughly enjoyed, and these cupcakes are no exception. They are dark chocolate, moist, and have the creamiest cream cheese icing in the world that goes perfectly with the chocolate. This is my go-to chocolate cupcake recipe, and being whole wheat is just a bonus. No flavor is compromised here because if I’m eating the calories that come packed in a cupcake…. it better taste delicious!

I love a cupcake that tastes like it came straight from a high end bakery. One that uses whole, real ingredients and yields a product far superior to cake mixes and trans fat laden whipped topping. There is something so much tastier about a product that comes right out of your own oven, and looks beautiful!These babies are truly classic and satisfying. If your sweet tooth is over powering your brain take a few minutes out of your day and treat yourself, your family will love you for it! 😉

Whole Wheat Chocolate Cupcakes with Cream Cheese Icing - Pretty Little Apron (1)

My secret ingredient in these: coffee! Coffee is going to do two things in this recipe. 1) Give your cupcakes a “dark chocolate” flavor and 2) give your cupcakes a light, fluffy texture. I didn’t even tell my husband I put coffee in these and guess what? He didn’t know because you can’t taste the coffee. It is simply there as a flavor booster and acid. Acidity in baking makes things lighter and fluffier so it is always a good thing (just like the buttermilk in your pancakes). When I make cupcakes I always include something acidic for this reason.

My other secret ingredient: orange zest in the cream cheese icing. I learned this trick almost immediately in pastry school. I can vividly remember the day… we were making Danish. Our instructor presented us with the option of using a filling she made and when I tasted it I just about melted. It was one of the best fillings I had ever tasted! I just had to know what was in it and she filled me in. Zest, zest, zest! ZEST! Orange zest will kick up the flavor of a cream cheese icing and take it to a whole ‘nother level! I mean a whole ‘nother level you’ve never known before! You have got to zest them oranges baby because that is the key to the *in Oprah voice* best EEEEVVVVEEEERRRR cream cheese icing!!!! So gimmicky of me, yet so true. Please excuse my gimmicky food blogger talk… because… you know that’s not my style! 😉

Whole Wheat Chocolate Cupcakes with Cream Cheese Icing - Pretty Little Apron (2)

Whole Wheat Chocolate Cupcakes with Cream Cheese Icing - Pretty Little Apron (3)

*Recipe measurements adapted from Death By Chocolate CupcakesbySally’s Baking Addiction.

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Whole Wheat Chocolate Cupcakes with Cream Cheese Icing

Whole Wheat Chocolate Cupcakes with Cream Cheese Icing - Pretty Little Apron (4)

By DanaPublished: August 18, 2014

  • Yield: 12 Servings

When the words "whole wheat chocolate cupcakes" come out of my mouth you are probably envisioning a dry, cardboard-like cupcake that …

Ingredients

  • 1 stick salted butter I use salted for extra flavor however you can use unsalted if you wish, just add 1/4 tsp salt to dry ingredients.
  • 1/4 cup semi-sweet chocolate chips I use Enjoy Life non-gmo mini chips
  • 3/4 cup whole wheat white flour I use King Arthur
  • 1/2 tsp baking soda
  • 3/4 tsp baking powder
  • 1/2 cup unsweetened coca powder
  • 2 eggs
  • 1/2 cup raw cane sugar can substitute regular sugar
  • 1/4 cup mascobado sugar can substitute brown sugar
  • 1 tsp vanilla extract
  • 1/2 cup strong brewed coffee
  • 1 8 ounce package cream cheese for icing
  • 1 stick butter (softened) for icing
  • 1/3 cup raw cane sugar for icing
  • 2 Tbsp water for icing
  • 1 Tbsp orange zest for icing
  • 1/2 tsp vanilla extract for icing

Instructions

  1. Put butter and chocolate in saucepan on stovetop over low heat and melt together while stirring frequently. Set aside to cool.
  2. Mix together dry ingredients including flour, baking soda, baking powder, and coca powder. If you use unsalted butter add 1/4 tsp of salt to dry ingredients. Set aside.
  3. Mix together sugar, eggs, vanilla, and cooled chocolate/butter mixture. Add 1/2 of the coffee to the wet ingredients, then 1/2 of the dry ingredients. Mix just to combine. Add the other half of the coffee followed by the other half of the dry ingredients and stir just to combine. Do not over mix batter as it will result in tough cupcakes!
  4. Line a cupcake pan with 12 cute paper liners and fill 3/4 of the way up with batter. Bake for about 17-18 minutes at 350 degrees or until a toothpick comes out clean.
  5. While cupcakes are baking beat (with paddle attachment) softened cream cheese and butter. It is really, really important that your butter and cream cheese are softened before you start!! Beat until very smooth, then switch paddle attachment out for whip attachment and whip cream cheese and butter. While whipping put sugar and water in saucepan over high heat on the stovetop. Allow sugar to melt without stirring. When sugar is bubbling and turns golden brown in color remove from heat and very slowly pour into cream cheese/butter mixture while continuing to whip. Your mixture may become slightly thin in consistency but continue to whip, and it will come together as it cools. Add vanilla extract and orange zest. Add addition 1-2 Tbsp raw cane sugar to taste to reach desired sweetness. Pipe icing onto cooled cupcakes using a piping bag fitted with a large tip, or a Ziplock baggie with the corner cut off. Enjoy!

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    Comments

    1. Whole Wheat Chocolate Cupcakes with Cream Cheese Icing - Pretty Little Apron (5)Thalia @ butter and brioche

      these cupcakes look delicious! love how relatively healthy the recipe is too.. definitely craving a cupcake right now!

    2. Whole Wheat Chocolate Cupcakes with Cream Cheese Icing - Pretty Little Apron (6)Yuvika

      I just made these – and they came out so well! Everybody in the family loved it – including my 2 year old!

    3. Whole Wheat Chocolate Cupcakes with Cream Cheese Icing - Pretty Little Apron (7)Melissa

      i’ve been baking from scratch for years and try to bake “clean.” This recipe is amazing, wonderful, and glorious! Everyone loved them and I loved, loved the fact they were whole wheat. They were just as good as my old stand by chocolate buttermilk cupcakes. I topped them with a peanut butter glaze made with PB2 (GMO free at least….) as I don’t care for a cream cheese frosting. Can’t wait to try more of your recipes. Whole Wheat Caramel Blondies and Unprocessed Hamburger Helper are going on next week’s menu! (Actualky, planning on getting molasses tomorrow so I can make the blondies.) Please, keep the better baking recipes coming!

    4. Whole Wheat Chocolate Cupcakes with Cream Cheese Icing - Pretty Little Apron (8)Brittany

      Just made these for my daughter’s 2nd birthday! They are delicious!!! I substituted Stevia powder for the raw cane sugar and they turned out fine. Thanks for the better alternative! Yum!

    Whole Wheat Chocolate Cupcakes with Cream Cheese Icing  - Pretty Little Apron (2024)

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