Healthy Chocolate Cupcakes
This post may contain affiliate links. As an Amazon Associate, I earn from qualifying purchases. Please read my disclosure.This is my favorite recipe for the softest, fluffiest healthy chocolate cupcakes. I’ve lightened them up with Greek yogurt, avocado, and coconut oil, and they’re incredibly easy to make. They’re the perfect feel-good treat my whole family loves, and best of all, they come together in just over 30 minutes.

My kids are huge fans of anything chocolate – from healthy hot cocoa to this chocolate oatmeal, so of course I had to come up with a cupcake recipe that’s extra chocolatey. And let me tell you, this one definitely delivers… ha! They’re lower in sugar, kid-friendly, and so rich and chocolatey you’d never guess they’re lightened up.
I’ve also used this cupcake recipe and topped it with my chocolate orange frosting, which is a fun way to switch things up. And if you and your kids like these, be sure to check out my peach cupcakes too or any of my low sugar desserts that kids love!
🌟 Why I Absolutely Love This Recipe
Chocolate cupcakes have always been one of my favorite desserts, and this recipe brings together two of my favorite things: rich chocolate flavor and a healthier twist. When my kids were toddlers, I wanted to give them sweet treats without all the sugar, but I couldn’t find any good recipes for healthy chocolate cupcakes made just for little ones. That’s exactly what inspired me to create these cupcakes!
When I think about giving a classic dessert a healthy twist, the first thing that comes to mind is cutting back on sugar. I knew I wanted to skip the processed sugar found in most cupcake recipes and replace it with something more wholesome. These cupcakes are sweet enough that your kids will still devour them, but without all the extra sugar and calories you find in typical baked treats. The key to making healthy chocolate cupcakes that both kids and adults will love is all about choosing smarter swaps.
In addition to cutting back on sugar, I swapped all-purpose flour for whole grains to boost the fiber and use healthier carbs. I also lightened things up by using Greek yogurt and skipping the butter and extra oil. And the frosting? It’s made with creamy avocado and sweetened with honey, making it so much better than traditional icing. Oh my… I promise these are seriously irresistible! They’re tender, chocolatey, and the kind of treat everyone, from toddlers to parents will love.
Latest Recipe Video!
🥘 Ingredients
I’ve broken up the ingredients below for the cupcakes and the frosting. While this recipe has several ingredients, I bet most of these are already in your pantry.

Coconut Oil: I always melt it before mixing it with the rest of the ingredients.
Eggs: I always make sure the eggs are at room temperature for the best results.
Plain Greek Yogurt: I like to make these healthy chocolate cupcakes with greek yogurt! I use Vegan Greek yogurt for a vegan substitution. If you do not need to substitute, any brand of plain greek yogurt will work.
Unsweetened Almond Milk: Any plant milk will work. I use unsweetened milk to keep the sugar to a minimum.
Honey: To make this healthy chocolate cupcake recipe vegan, I’ll use maple syrup or my vegan honey.
Unsweetened cocoa powder: This ingredient is critical for that deep chocolate flavor in these sugar free cupcakes for toddlers and kids.
White Whole Wheat Flour: White whole wheat flour is made from white wheat (vs. red wheat for whole wheat flour), and has a lighter taste and texture (similar to all purpose flour), but is equivalent to whole wheat flour from a nutritional standpoint! Whole wheat pastry flour would also work well in this recipe. I use Gluten Free 1:1 Baking Flour for a gluten-free option.
Baking Powder & Salt: The salt enhances the other flavors in the recipe, while the baking powder gives the healthy kids cupcakes a light and fluffy texture.
Avocado: The secret ingredient in this frosting instead of cream cheese! The avocado makes this frosting smooth and creamy.
👩🏽🍳 How To Make
Making my low sugar healthy chocolate cupcakes for my kids and topping them with that rich, creamy frosting is one of my favorite things to do. It’s such a fun (and tasty) little baking activity we all enjoy together. Here’s how I make them:
Prep The Tin: First, I line a muffin tin with paper cupcake liners and set that aside. Depending on the type of liners I am using, sometimes I will spritz them with avocado oil spray. Your preferred baking spray will work too. Silicone liners don’t usually require spraying, but you can still spray them to make sure the cupcakes don’t stick.
Mix Wet Ingredients: In a large bowl, I mix together melted coconut oil and eggs. Then, I add Greek yogurt, almond milk and honey to the same bowl and give it all a good mix.

Mix Dry Ingredients: In a smaller bowl, I’ll whisk together cocoa powder, wheat flour, baking powder and salt.

Then, I combine the wet and dry ingredients in a larger bowl and mix well.

Add Cupcake Batter To Tin: I’ll ladle the cupcake batter into each section of the muffin tin, filling it about 2/3 of the way.

Bake: I bake these in a 350 degrees Fahrenheit oven for 20-22 minutes or until a toothpick inserted into the center comes out clean. Allow the cupcakes to cool completely before adding the frosting.
Make The Frosting: While the cupcakes are baking and cooling, I’ll make the frosting. First, I’ll peel the avocado and add the remaining frosting ingredients to a large bowl.

Mix the ingredients: I use an electric mixer on low speed and beat everything together until it’s smooth and creamy. It only takes a minute, and the texture comes out perfect every time.

Frost Cupcakes: When the cupcakes have cooled completely, I’ll use an offset spatula to frost each cupcake. Pastry bags or zip top bags are also a quick and easy way to frost cupcakes. From there, feel free to add on any toppings you like.

Serve and enjoy: Once the cupcakes are frosted, I hand them out and watch the smiles appear. They’re always a hit, and we never have leftovers for long.

💭 Expert Tips
My #1 Secret Tip for this healthy chocolate cupcakes recipe is to bring the cupcake ingredients to room temperature, especially before combining the eggs and coconut oil. Since the coconut oil requires melting, allow it to cool before adding the eggs. Otherwise, the eggs may “cook” when added to the warm oil and scramble.
Other Tips To Keep In Mind:
- Sweetness level: These cupcakes lean more toward a dark chocolate flavor. If you want them sweeter, I just add a little extra honey to both the batter and the frosting.
- Cupcake liners: I always spray my liners well so the cupcakes don’t stick. Silicone liners work great and usually need less spray than paper ones.
- Measuring tip: I like to spoon and level my flour and cocoa powder into the measuring cup. It helps keep the cupcakes light and fluffy every time.
- Do not overmix: I mix just until the wet and dry ingredients come together. Overmixing makes the cupcakes dense, so I always stop as soon as it’s combined.
📖 Variations
There are several different ways to alter this recipe so vegan or gluten-free kiddos can enjoy this recipe, too.
Chocolate Cupcakes With No Milk: I swap the cow’s milk for almond milk or any plant-based milk. Just make sure to choose an unsweetened variety so you can avoid added sugar.
Egg-Free Cupcakes: I simply swap the eggs for what’s known as “flax eggs.” For each egg, swap it for 1 tablespoon ground flax seeds mixed with 3 tablespoons of water. Let the mixture sit for at least 10 minutes and then just mix it into the batter the way you would regular eggs.
Make This Recipe Vegan & Dairy-Free: In addition to switching the eggs for flax eggs, I also substitute the Greek yogurt for vegan Greek yogurt and honey for maple syrup or agave.
Mini Cupcakes: To turn these into mini healthy cupcakes for toddlers, I fill each mold 1/2 full instead of two-thirds.
🧁 Healthy Cupcake Toppings
Sometimes I like to create a toppings bar for my kids so they can decorate their own cupcakes after we frost them! Here are some of my favorite healthy toppings:
Fresh Or Dried Fruit: Fresh blueberries, raspberries or even sliced strawberries all work well, or try diced dried apricots or dates. You can also crush up some freeze-dried raspberries, strawberries, mangoes, or bananas and sprinkle them on top.
Crunchy Toppings: Try coconut flakes, cacao nibs, chopped nuts (almonds, walnuts, and pecans all work well), roasted pumpkin seeds, dark chocolate shavings, or my low sugar granola!
Nut Butter Drizzles: Almond butter, cashew or peanut butter add richness and healthy fats without any refined sugar.
🍽 Serving Suggestions
Healthy cupcakes are delicious served as is. I’ll use them for a healthy dessert for my kids, but they’re also great served at birthday parties or other special occasions. I also like to tuck this in snack boxes for a plane ride or a road trip as a sweet little surprise. If you’re looking to add them to a bigger spread, here are a few other dishes to help you out.
Fruit: I try to balance out the sweet treats with wholesome dishes. I like to serve this with a healthy fruit salad or my easy fruit filled pancake tacos.
Beverages: Wash these delicious cupcakes down with a refreshing strawberry milk tea, or a broccoli smoothie to add some veggies with a sweet treat.
Other Desserts: What’s a delicious cupcake served without ice cream? A big scoop of my vegan matcha icecream, or this delicious chocolate banana ice cream would be a decadent indulgence.
🧊 Storing And ♨️ Reheating
I’ve broken down storage options for unfrosted and frosted cupcakes below. Remember to allow the healthy toddler cupcakes to cool completely before storing. This prevents condensation from forming, which can make them soggy.
Refrigeration: For longer storage (up to a week), I’ll place the airtight container of frosted or unfrosted cupcakes in the refrigerator.
Room Temperature: To store at room temperature, I’ll place the cooled cupcakes in an airtight container. I have used either a plastic container with a tight-fitting lid or a resealable plastic bag – both will work. Store the container at room temperature if you plan to eat the cupcakes within 1-2 days. Keep them in a cool, dry place away from direct sunlight and heat.
Since the frosting in this recipe is stable, frosted cupcakes can also be stored at room temperature for up to 1-2 days, following the steps above.
Freezing: When freezing, I wrap each unfrosted cupcake individually in plastic wrap or aluminum foil, then place them in a freezer-safe airtight container or resealable bag and freeze for up to 3 months. To thaw, I leave the cupcakes at room temperature for a few hours or overnight.
I do not recommend freezing frosted cupcakes as the frosting may separate during thawing.
❓Recipe FAQs
I always look for an avocado that’s dark green and has a slight give when I gently squeeze it. If it’s not ripe enough, it won’t blend well and the frosting turns out chunky. And if it’s too ripe, it can make the frosting watery, which is not what I want.
For the frosting: Mash the avocado thoroughly with a fork until smooth. Then, whisk in the other ingredients until well combined.
For the batter: Use a whisk, spoon, or spatula to add the dry ingredients to the wet ingredients. Work a little at a time until just combined.
This method may take a bit longer but can achieve a smooth consistency.
I like to pop the frosting in the fridge for about 15 to 30 minutes before using it. Chilling helps it firm up nicely, especially if the avocado or coconut oil has softened a bit too much.
The secret to moist cupcakes is all about getting the right balance of eggs, milk, and oil. Eggs and almond milk keep the cupcakes tender and moist, while the coconut oil adds that soft, rich texture. For this recipe, I really focused on getting that ratio just right so every bite is soft and satisfying.

🥣 More Healthy Dessert Recipes!
Love this Healthy Dessert recipe? Please leave a 5-star rating 🌟 in the recipe below and/or a review in the comment section further down the page!
You can also FOLLOW ME on FACEBOOK, INSTAGRAM, and PINTEREST to see more delicious, healthy, family-friendly food, and if you have any questions, I’m here to help!
📋 Recipe Card
🎥 Watch How to Make It
Healthy Chocolate Cupcakes
Ingredients
For The Cupcakes
- 2 tbsp coconut oil melted
- 2 large eggs, room temperature flax eggs for vegan
- ¼ cup Greek yogurt vegan Greek yogurt for vegan substitution
- ½ cup almond milk
- 3-6 tbsp honey or maple syrup (for a vegan option) Note: Use 3 tbsp for these cupcakes to have 8 grams of sugar a piece. Use up to 6 tbsp for a sweeter cupcake.
- 1 cup unsweetened cocoa powder
- ¾ cup white whole wheat flour (1:1 gluten free baking flour for gluten-free option)
- 2 tsp baking powder
- ¼ tsp salt
For The Healthy Chocolate Frosting:
- 1 large, ripe avocado
- 1 tbsp coconut oil
- ⅓ cup unsweetened cocoa powder
- 2-4 tbsp honey (maple syrup for a vegan option) Note: Use 2 tbsp for these cupcakes to have 8 grams of sugar a piece. Use up to 4 tbsp for a sweeter frosting.
- 1 tbsp almond milk
Equipment
- Electric Hand Mixer
Instructions
To Make The Cupcakes:
- Preheat oven to 350 degrees F and line a muffin tin with paper cupcake liners.
- In a large bowl, mix together melted coconut oil and eggs.
- Add Greek yogurt, almond milk and honey. Mix to combine.
- In a smaller bowl, whisk together cocoa powder, wheat flour, baking powder and salt.
- Slowly add dry ingredients to wet ingredients.
- Scoop cupcake batter into each section of the muffin tin, filling it about 2/3 of the way.
- Bake for 20-22 minutes. Allow to cool before adding frosting.
For The Frosting:
- Add all ingredients to a large bowl.
- Use an electric mixer to beat on low speed until smooth.
- Use an offset spatula to frost each cupcake.
Notes
- My #1 Secret Tip for this healthy chocolate cupcakes recipe is to bring the cupcake ingredients to room temperature, especially before combining the eggs and coconut oil. Since the coconut oil requires melting, allow it to cool before adding the eggs. Otherwise, the eggs may “cook” when added to the warm oil and scramble.
- Sweetness level: These cupcakes lean more toward a dark chocolate flavor. If you want them sweeter, I just add a little extra honey to both the batter and the frosting.
- Cupcake liners: I always spray my liners well so the cupcakes don’t stick. Silicone liners work great and usually need less spray than paper ones.
- Measuring tip: I like to spoon and level my flour and cocoa powder into the measuring cup. It helps keep the cupcakes light and fluffy every time.
- Do not overmix: I mix just until the wet and dry ingredients come together. Overmixing makes the cupcakes dense, so I always stop as soon as it’s combined.
wow those sounds like they came for a 5 star NYC bakery the ingredients are fabulous hope your selling these 🙂 outstanding!
Haha thanks Claudia! Enjoy!
I really want to try the avocado frosting. It looks delicious!
Yes!! It’s so rich and creamy – you won’t even be able to tell there is avocado in it!
These look delicious. That avocado frosting sounds amazing.
Thanks Dannii! I’m sure you will love these when you try them!
Love when I can have chocolate treats without the guilt!
Totally!! You can literally have your cake and eat it too! 🙂
I love your healthy approach to make cupcakes. The recipe sounds amazing, and it is worth trying. 🙂
Thank you so much Irina!! I’m sure you’ll love this recipe!
Looks mouth watering! I can’t wait to try it!
Thanks Jackie! I’m sure you will love these delicious cupcakes!
I couldn’t resist myself looking at these cupcakes! They look so delicious.
Thank you so much Mitchell! I’m sure you will love them if you make them at home!