These healthy chocolate cupcakes are fluffy and lighter thanks to veggie puree instead of eggs and oil found in traditional cupcakes. The easy one bowl recipe is perfect for kid's who like to bake. The perfect healthy cupcake from scratch.
When you think of making a healthy chocolate cupcake recipe from scratch, rarely does the word "healthy" pop into your mind. But what makes my easy chocolate cupcakes healthy is the use of pumpkin puree or sweet potato puree, instead of eggs and oil. And no, you will not taste vegetables. One bite of a fluffy cupcake, and you will only taste moist fluffy dark chocolate cake.
Like my other cupcake recipes, these are free of many things, free of oil, gluten, nuts, dairy, and eggs. If you are searching for refined-sugar-free as well, try my brownie recipes, most use date paste as a sweetener.
You'll Love This Healthy Cupcake
This fluffy gourmet chocolate cupcake is so easy to make, just toss ingredients in a bowl, bake and frost. I share my awesome chocolate buttercream frosting recipe in this post, or you can use my super healthy 2-ingredient sweet potato chocolate frosting, my white frosting, or my buttercream frosting recipe which provides healthier ways to color frosting.
These cupcakes are lighter in texture, and perfect for anyone wanting a fancy chocolate cupcake that is healthier. The recipe is also suitable for vegans, and those on a dairy free or gluten free diet.
Ingredients
These cupcakes are moist with a soft tender crumb, and a deep chocolate flavor that you can even eat them without a frosting, muffin style. And they are easy to customize into a peppermint cupcake by adding extract to both the batter and frosting. You probably have the ingredients right now. Take a look:
- All-purpose flour. Or use gluten-free baking flour. My chocolate fudge cake uses oat flour if you'd prefer to try that recipe.
- Unsweetened cocoa powder. Use unsweetened and the higher the quality, the better the cupcake. Dutch-processed works well.
- Organic cane sugar. Regular cane sugar works but this tastes better.
- Almond milk + lemon juice. Helps with leavening.
- Pumpkin puree. Works to provide support an egg would and replaces oil.
- Aquafaba or apple sauce. Either works as an egg replacer.
- Leaveners & flavorings: baking powder, baking soda, coffee, vanilla extract, salt
Steps To Bake
1. Line your cupcake pans with paper liners and preheat your oven to 350 F.
2. Mix wet ingredients in a large bowl, and stir with hand-mixer or spoon until combined.
3. Add dry ingredients and stir or mix just enough to combine. Don't over-stir or you'll create a "tough" cupcake.
4. Fill each cupcake liner about ¾ full and bake for 18 minutes at 350 F.
5. Let them cool in pan for 5 minutes and then transfer to rack to cool.
Pro-tip: Scoop using a medium-sized ice cream scoop for the perfect amount per cupcake liner. That way you avoid adding too little which results in a dry cupcake, or too much which spills over and sticks to the pan.
How Are These Cupcakes Healthy?
It's easy to make cupcakes healthier. Here is how:
1. Be sure to make your cupcakes from scratch. From scratch baking is easy, just combine ingredients, bake and eat. Just as easy as a box mix and far healthier because you can control the ingredients and vastly reduce processed additions.
2. Use a vegetable puree such as pumpkin or sweet potato instead of processed oil. I also use aquafaba or unsweetened apple sauce instead of eggs. Eggs are not unhealthy but they are not vegan and all my recipes are vegan so I never use eggs.
3. I keep sugar low in all my recipes, and I use organic cane sugar which has no bone char and is fair trade which means workers who package the product are treated fairly.
Variations & Substitutions
1.The veggie puree can be pumpkin puree, sweet potato puree, butternut squash puree or even zucchini puree. You can get quality versions of most of these canned, or if you don't mind the extra step, use fresh by steaming the vegetable and pureeing in a food processor.
2. Flavors can be added to these cupcakes via extract. For instance, I frost these with white frosting during the holidays and add peppermint extract in both the batter and the frosting to make festive peppermint cupcakes.
Recipe Tips
1.Be sure all your ingredients are at room temperature to start. Anything hot or cold can change the texture of your healthy chocolate cupcake.
2.When you are dissolving the sugar, mix and mix until you are sure the sugar has dissolved - there will be a minimal crunch when you press your spoon against the bowl. Dissolved sugar helps keep the healthy cupcake light.
3.Don’t over. Don't over stir, don't over bake, and don't leave the cupcakes too long in the hot pan to cool.
FAQS
How to make homemade buttermilk for cake recipes
You don't need to buy buttermilk for this chocolate cupcake recipe. Just add lemon or apple cider vinegar to milk and wait a few minutes. That is a healthy vegan form of homemade buttermilk.
Can I make these cupcakes as a cake?
A similar recipes for a chocolate fudge cake can be found here.
Can I make these cupcakes gluten-free?
Yes, use a gluten free baking flour and add 1 tablespoon of cornstarch or arrowroot to help stabilize them.
Is there an egg substitute for these health cupcakes?
Yes, this recipe uses pumpkin puree instead of eggs and oil.
How do I prevent my cupcakes from sticking to the cupcake liners?
Use parchment baking cups, and rub a bit of coconut oil into each liner, or spray with a little cooking spray. Let your cupcakes cool before peeling them off.
Other Healthy Cupcakes & Cakes
- Chocolate Dipped Cupcakes (hi tops)
- Healthier Lemon Cupcakes
- Hot Chocolate Cupcakes
- Dairy Free Chocolate Cake
- Fluffy Vegan Vanilla Cake
I'd like to invite you to sign up for my free chocolate course. Five lessons hit your inbox with detail on how to create your own simple healthy chocolate desserts.
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📖 Recipe

Healthy Chocolate Cupcakes
Ingredients
Cupcake Dry Ingredients
- 1 ½ cups all-purpose flour or a GF baking flour
- ½ cup unsweetened cocoa powder use dutch processed for darker color
- 1 cup organic cane sugar
- 1 tablespoon coffee use instant granules or fresh brewed
- 1 teaspoon baking powder
- 1 teaspoon baking soda
- ½ teaspoon salt
Cupcake Wet Ingredients
- 1 cup dairy-free milk
- 1 tablespoon lemon juice
- ⅓ cup pumpkin puree, canned (Or sweet potato puree)
- 3 tablespoon aquafaba, the liquid from a can of chickpeas or apple sauce
- 2 teaspoon vanilla extract
Chocolate Frosting:
- 4 cups organic powdered sugar
- 1 cup unsweetened cocoa powder dutch processed cocoa for darker color
- 1 ½ sticks vegan butter
- 2 teaspoon vanilla extract
- 5 tablespoon dairy free milk
Useful Equipment
Instructions
Prep
- Preheat your oven to 350 F.
- Measure out aquafaba (liquid from a can of unsalted chickpeas or garbanzo beans) OR use unsweetened apple sauce.
- Line cupcake pan with 12 paper liners.
- Activate your milk by adding lemon juice to it and let it sit for 5 minutes.
Make cake
- To the large mixing bowl, add wet ingredients and sugar, and mix until combined.1 cup dairy-free milk, 1 tablespoon lemon juice, ⅓ cup pumpkin puree, canned, 3 tablespoon aquafaba, the liquid from a can of chickpeas, 2 teaspoon vanilla extract, 1 cup organic cane sugar
- Then add the dry ingredients and mix until combined.1 ½ cups all-purpose flour, ½ cup unsweetened cocoa powder, 1 tablespoon coffee, 1 teaspoon baking powder, 1 teaspoon baking soda, ½ teaspoon salt
- Distribute the batter evenly into 12 cupcake liners using a medium cookie scoop.
- Bake cupcakes for 18 minutes. Or until tester comes out clean for all of them.
- Let them cool for a ten minutes in pans, then put cupcakes on cooling rack and allow to cool completely before frosting.
Make frosting
- Add powdered sugar, cocoa powder, vegan butter, vanilla extract and 2 tablespoon of the milk to a large mixing bowl. If butter is cold, microwave it for 10 seconds to soften.4 cups organic powdered sugar, 1 cup unsweetened cocoa powder, 1 ½ sticks vegan butter, 2 teaspoon vanilla extract, 5 tablespoon dairy free milk
- Use a hand-mixer or an electric mixer to combine. Add the remaining milk gradually until you have a creamy consistency. You can add more or less milk, but be careful, it can turn too liquidy very fast.
- Add frosting to a frosting bag with your chosen tip.
- Frost cupcakes
Store
- To store cupcakes in the freezer for a month, pack them unfrosted in a sealed container.Once frosted, the cupcakes are fine at room temperature for about 3 days and then they begin to dry out.
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