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These homemade mini chocolate cupcakes are packed with rich chocolate flavor in bite-sized form! Made with protein-rich Greek yogurt and filling whole wheat flour, they’re a healthy treat your whole family will love!
Whole Wheat Chocolate Cupcakes with Cream Cheese Frosting
These low sugar mini chocolate cupcakes are definitely not what you think of when you imagine healthy cupcakes! Moist, fluffy, and tender, these little bites really are like the real thing.
Plus, you can make this mini chocolate cupcake recipe in one bowl using your hand mixer, so it’s quick and easy!
Don’t forget to make a batch of this amazing naturally sweetened frosting. It’s the perfect delicious topping for your little cupcakes!
MINI CHOCOLATE CUPCAKES
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Why We Love This Mini Chocolate Cupcakes Recipe
- Moist & tender: Thanks to a little Greek yogurt, these fluffy chocolate cupcakes are soft and tender, making them wonderful to eat!
- One bowl recipe: Who wants to make a big mess before a birthday party or special gathering? Fortunately, these easy chocolate cupcakes with yogurt are all made in one bowl to keep the mess to a minimum.
- Low Sugar: With only 2 grams of sugar per cupcake (plus frosting), these homemade low sugar chocolate cupcakes won’t cause the same sugar spike in your little ones as your typical cupcakes. No sugar crash here!
Ingredient Notes
- Coconut oil: Instead of butter or vegetable oil, let some coconut oil soften at room temperature. It incorporates a delicious flavor into the cupcakes.
- Coconut sugar: Coconut sugar is the easiest way to sweeten these mini chocolate cupcakes. You can also substitute brown sugar for a similar flavor and texture.
- Eggs: For best results, use room-temperature eggs when baking.
- Greek yogurt: Choose plain Greek yogurt to add moisture and tenderness to these mini cupcakes. We used 2%, but any fat percentage can be used.
- Milk: Use milk to thin out the cupcake batter. You can also use your favorite milk alternative.
- Vanilla extract: Vanilla highlights all the different scents and flavors in this mini chocolate cupcake recipe to make the cupcakes even more enticing.
- White whole wheat flour: This flour is higher in fibre, making it more filling, yet it tastes just like regular flour!
- Unsweetened cocoa powder: Natural cocoa powder will add a deep chocolate flavor to this great recipe without any extra sugar, unlike regular chocolate.
- Baking powder: Baking powder will help your batter rise in the oven, creating the perfect tender texture.
- Baking soda: Baking soda is one of three leavening agents in this easy recipe to make sure every cupcake is light and fluffy!
- Salt: A little salt will help your baking soda get to work and draw out the sweetness from all your other ingredients.
How to Make Chocolate Mini Cupcakes from Scratch
- Preheat the oven to 350 degrees F and line a mini muffin tin with paper liners. Set aside.
- In a medium bowl, beat the coconut oil and sugar with a handheld electric mixer until light and fluffy, about 1 minute. Add the eggs, one at a time, then the Greek yogurt, milk and vanilla.
- Slowly add in the flour, cocoa powder, baking powder, baking soda, and salt. Stir gently with a spoon until just combined. Divide the batter among the mini cupcake liners or mini silicone cupcake tray filling about 3/4 of the way full.
- Bake for 11-13 minutes or until inserted toothpick comes out clean.
- Remove from oven. Remove cupcakes from pan and let them cool completely on a wire rack.
- Frost using desired frosting.
Keep scrolling to the recipe card below for the full printable recipe!
RECIPE TIPS
- For the best rise, chill your cupcake batter in the fridge for 30 minutes to an hour. This can help make sure you get an even rise in the oven, too.
- You can substitute melted butter or vegetable oil for the coconut oil.
- For real chocolate lovers, stir mini chocolate chips into the batter.
- Sour cream is a great substitute for Greek yogurt in baking.
- If you want to serve these mini cupcakes without frosting, consider sprinkling a little extra coconut sugar on top for a nice crunch.
- Be careful not to overbake these mini cupcakes or they will become too dry.
- For an even rise, it can be helpful to sift the dry ingredients before you add them to the mixing bowl.
- To make it easy to fill your mini muffin pan, add your batter to a piping bag and fill the cups using that.
Recipe FAQs
What frosting goes with chocolate cupcakes?
My very favorite frosting to use on this moist chocolate cupcake is my chocolate frosting without powdered sugar! Naturally sweetened with dates, it’s perfectly sweet and creamy with no added sugar.
Since chocolate is so versatile though, you could easily top these with this 2-ingredient chocolate frosting, peanut butter frosting, vanilla buttercream, cinnamon frosting, and more.
How long to bake mini cupcakes?
Since they cook so quickly, you only need to make your mini chocolate muffins for about 11-13 minutes in an oven preheated to 350 degrees F.
How do you ice cupcakes for kids?
The easiest way to decorate these mini chocolate cupcakes for kids is to use a piping bag. This will give you greater control over the frosting, and tends to have a nicer presentation. If you’re baking a bunch of cupcakes for birthday parties or other events, this is also much faster than using a palette knife or offset spatula!
Storage Guidelines
- Store any leftover mini chocolate chip cupcakes in an airtight container at room temperature for up to a week.
- You can easily freeze leftover muffins to enjoy later (ideally unfrosted). Just let them cool to room temperature, then place them in a freezer-safe bag. They’ll stay fresh for several months. Let the cupcake thaw in the fridge for a few hours and serve!
Mini Chocolate Cupcake Topping Ideas
There are so many ways to decorate these mini chocolate cupcakes! You can also create a little cupcake decorating bar with a bunch of different toppings and sprinkles!
- Chocolate cream cheese frosting
- Vanilla frosting
- Chocolate buttercream
- Peanut butter frosting
- Sprinkle with coconut sugar before baking
- Drizzle with melted chocolate
- Regular or naturally dyed sprinkles
- Fresh berries
- Mini chocolate chips
Recipe Variations
- Zucchini: For a little extra fibre, add 1/4 cup shredded zucchini. Let the zucchini sit in a strainer for 20-30 minutes and squeeze to remove excess liquid.
- Chocolate chips: Stir mini chocolate chips into the batter for a little sweetness and crunch.
- Peanut butter: Sub in 1-2 tablespoons of peanut butter for the coconut oil for a peanut butter chocolate flavor!
More Healthy Treats
- 3-Ingredient Banana Brownies
- Healthy Smash Cake
- Baked Chocolate Chip Oatmeal
- 3-Ingredient Cookies {No Egg}
- No Sugar Added Muffins
- Apple Banana Carrot Muffins
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Mini Chocolate Cupcakes {Whole Wheat, Low Sugar}
Servings: mini cupcakes
These homemade mini chocolate cupcakes are packed with rich chocolate flavor in bite-sized form! Made with protein-rich Greek yogurt and filling whole wheat flour, they’re a healthy treat your whole family will love!
Ingredients
- 1/4 cup coconut oil (softened at room temperature)
- 1/3 cup coconut sugar (or sub in brown sugar)
- 2 large eggs
- 3/4 cup milk or milk alternative
- 1/2 cup plain Greek yogurt
- 2 teaspoons vanilla extract
- 3/4 cup white whole wheat flour
- 1/4 cup unsweetened cocoa powder
- 1 teaspoon baking powder
- 1/4 teaspoon baking soda
- 1/4 teaspoon salt
For Frosting (optional)
Instructions
- Preheat the oven to 350 degrees F. Spray a mini muffin tin with cooking spray or line it with paper liners. A mini silicone cupcake tray works well too. Set aside.
- In a medium bowl, beat the coconut oil and sugar with a handheld electric mixer until light and fluffy, about 1 minute. Add the eggs, one at a time, then the milk, Greek yogurt, and vanilla.
- Slowly add in the flour, cocoa powder, baking powder, baking soda, and salt. Stir gently with a spoon until just combined.
- Divide the batter into the mini cupcake liners or mini silicone cupcake tray filling about 3/4 of the way full.
- Bake for 11-13 minutes or until inserted toothpick comes out clean.
- Remove from oven. Remove cupcakes from pan and let them cool completely on a wire rack.
- Frost using desired frosting.
Notes
- For the best rise, chill your cupcake batter in the fridge for 30 minutes to an hour. This can help make sure you get an even rise in the oven, too.
- You can substitute melted butter or vegetable oil for the coconut oil.
- For real chocolate lovers, stir mini chocolate chips into the batter.
- Sour cream is a great substitute for Greek yogurt in baking.
- If you want to serve these mini cupcakes without frosting, consider sprinkling a little extra coconut sugar on top for a nice crunch.
- Be careful not to overbake these mini cupcakes or they will become too dry.
- For an even rise, it can be helpful to sift the dry ingredients before you add them to the mixing bowl.
- To make it easy to fill your mini muffin pan, add your batter to a piping bag and fill the cups using that.
Nutrition
Calories: 46kcal | Carbohydrates: 5g | Protein: 2g | Fat: 3g | Saturated Fat: 2g | Polyunsaturated Fat: 0.1g | Monounsaturated Fat: 0.3g | Trans Fat: 0.001g | Cholesterol: 13mg | Sodium: 58mg | Potassium: 35mg | Fiber: 1g | Sugar: 2g | Vitamin A: 28IU | Calcium: 25mg | Iron: 0.3mg
