Healthy Chocolate Cupcakes with Honey Avocado Frosting

This post may contain affiliate links. As an Amazon Associate, I earn from qualifying purchases. Please read my disclosure.

These are the best healthy chocolate cupcakes ever!! They are lightened up with Greek yogurt, white whole wheat flour, and contain no refined sugar. Super easy to make, moist, rich and chocolatey – the perfect guilt-free treat for the whole family!

For those of you who know me, you know that cupcakes are one of my favorite desserts 🙂 And chocolate cupcakes combine TWO of my favorite things!

Which is why, I had to come up with a way to make the best healthy chocolate cupcakes so I could enjoy these delicious treats much more often.

This recipe comes together in just over 30 minutes with simple, clean ingredients. And these cupcakes are topped with a healthy cupcake frosting made with avocados instead of cream cheese!

Latest Recipe Video!

This cupcake recipe is super easy to make, low in sugar, and still super decadent and chocolatey! I’ve also included notes on substitutions for different dietary restrictions that all work really well.

You have to try these low fat cupcakes the next time you have a craving for chocolate cupcakes. I can guarantee that everyone who tastes them will love them!

Refined Sugar-Free Chocolate Cupcake Recipe

I don’t know about you, but when I think of how to put a healthy twist on a classic dessert, my mind goes straight to sugar. So I knew I wanted to get rid of the processed sugar in most cupcake recipes, and replace it with a healthier option. 

That’s where these honey chocolate cupcakes come in. They’re sweet enough that your kids will still devour them but without the insane amount of processed sugar and calories found in most baked treats.

Recipe Ingredients & Notes

Chocolate Cupcake Ingredients

• Coconut Oil: You’ll want to melt it before mixing it with the rest of the ingredients.
• Eggs (use Flax Eggs for a vegan substitution): At room temperature
• Plain Greek Yogurt (use Vegan Greek yogurt for a vegan substitution)
• Unsweetened almond milk (or any plant milk)
• Honey (use maple syrup for a vegan option)
• Unsweetened cocoa powder: Critical for that deep chocolate flavor!
• White Whole Wheat Flour (use Gluten Free 1:1 Baking Flour for a gluten-free option). 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.
• Baking Powder & Salt

Healthy Cupcake Frosting

• Avocado: The secret ingredient in this frosting instead of cream cheese!
• Coconut Oil
• Unsweetened Cocoa Powder
• Honey (or maple syrup for a vegan option)
• Unsweetened almond milk

How to Make Healthy Chocolate Cupcakes Step by Step

Step 1: 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.

Step 2: Add Greek yogurt, almond milk and honey. Mix to combine. In a smaller bowl, whisk together cocoa powder, wheat flour, baking powder and salt.

Step 3: Slowly add dry ingredients to wet ingredients.

Step 4: Scoop cupcake batter into each section of the muffin tin, filling it about 2/3 of the way.

Step 5: Bake for 20-22 minutes. Allow to cool before adding frosting.

Directions for the Frosting

Step 1: Add all ingredients to a large bowl.

Step 2: Use an electric mixer to beat on low speed until smooth.

Step 3: Use an offset spatula to frost each cupcake.

How to Make Chocolate Cupcakes Healthier 

The key to making guilt-free chocolate cupcakes is choosing smarter swaps.

Here are some of the changes we made to make these healthy chocolate cupcakes:

• Whole Grains: Switching out all purpose flour for a whole grain flour adds fiber and healthier carbs into this chocolate cupcake recipe
• Less Sugar: We used a little less than half the amount of sugar in most traditional cupcake recipes!
• Less Fat & Calories: Subbing in Greek yogurt and removing butter/oil from the recipe takes down the fat and calories in each cupcake.
• Healthy Cupcake Icing: A cupcake is nothing without its gloriously creamy icing, right? Unfortunately, it’s basically nothing but sugar in regular cupcakes. We swapped the icing for healthy cupcake frosting – made with an avocado, honey, and coconut oil mix, and I must say it turned out incredible!

Frequently Asked Questions

Recipe Variations

Change Up The Milk

Many people want chocolate cupcakes with no milk, so what I’ve done here is swap the milk for almond milk.

Almond milk is a good alternative for those who don’t drink cow’s milk. It contains no cholesterol and has less saturated fat than whole milk. Almond milk contains only about 30 calories for a cup and is an excellent source of vitamin E.

Make it Egg Free

To make egg-free cupcakes, simply swap the eggs for what’s know as “flax eggs.” For each egg, swap it for 1 tablespoon ground flaxseeds mixed with 3 tablespoons of water.

Make it Vegan

1. Substitute the Eggs for Flax Eggs
2. Substitute the Greek Yogurt for Vegan Greek Yogurt
3. Substitute the Honey for Maple Syrup or Agave

Change the Sugar

When it comes to choosing a healthier sugar alternative for cupcakes, I personally prefer honey, but you can also use maple syrup or even agave. 

Make it for Kids!

While kids will love these low fat chocolate cupcakes the way they are, to turn these into mini healthy cupcakes for toddlers, just fill each mold 1/2 full instead of two-thirds. 

Top Tips for Making Healthy Chocolate Cupcakes

• These cupcakes are not meant to be overly sweet – they taste more like dark chocolate. If you want a sweeter cupcake, add a bit more honey to the cupcake batter and the frosting.
• Make sure to spray your cupcake liners with cooking spray so the cupcake doesn’t stick to the liner after baking!
• Spoon and level your flour and cocoa powder into your measuring cup vs. using your measuring cup to scoop out the flour. You’ll get a more accurate measurement that way and a lighter/fluffier cupcake!
• Make sure your ingredients are at room temperature for easy mixing and for a better tasting cupcake.
• Don’t overmix! Mix the batter together just until the wet and dry ingredients are combined. Overmixing results in a tough cupcake!

Well, I think I pretty much covers everything. This easy cupcake recipe has quickly become one of my favorite healthier chocolate desserts. I hope you give it a try!

Want More Healthy Cupcakes And Treats? Check These Out:

• Healthy Blueberry Cupcakes
• Lightened Up Red Velvet Cupcakes 
• 30 Low Sugar Desserts