by Olena

Healthy Chocolate Muffins

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Olena Osipov
5 from 24 votes

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Healthy Chocolate Muffins with Greek yogurt, applesauce, whole wheat flour, cacao powder and honey. Kids absolutely love these fudgy and nutritious muffins.

This muffin recipe is a delicious chocolate-y cross between my healthy chocolate bread and healthy chocolate cake.

Healthy chocolate muffins in a muffin tin

Whole Wheat Chocolate Muffins

I had no plans to post these healthy chocolate muffins as I was preparing them for kids’ and Alex’s lunch boxes for the week. I guess I was wrong: 12 muffins were gone in 4 hours between 4 of us and in the morning kids were super upset none made to their lunch boxes.

They obviously love healthy chocolate chip muffins and these healthy chocolate chip cookies but never I expected such demand for these chocolate muffins with Greek yogurt and applesauce. I remade them yesterday and 5 muffins were gone still piping hot – my oldest one had a friend over and between 2 of them they ate 5 muffins. Seriously, what’s up with these muffins?!

These chocolate muffins are as good as chocolate bars and healthy chocolate ice cream! Indulgently fudgy, moist and chocolate chip loaded.

My word of advice when making these chocolate muffins. Make a double batch! You won’t regret it. At my house, these muffins are gone before they have even cooled down!

Ingredients for Healthy Chocolate Muffins

  • Eggs: One time I ran out of eggs and used 1 large egg + 3 tbsp ground flaxseed soaked in 6 tbsp warm water for 10 mins. Which makes a vegan egg replacer. Very moist and fudgy results – try that.
  • Applesauce and Greek yogurt: You do need to use both and one cannot be substituted for another.
  • Maple syrup or honey: Baking is a science and unfortunately you can’t substitute wet sweetener with powdered as it will offset liquid:dry ingredients ratio and recipe will not turn out.
  • Cacao or cocoa powder
  • Whole wheat flour or spelt flour: Chocolate muffin recipe will not work with any other flour because again “baking is a science”.
  • Baking essentials: Baking powder, baking soda, salt.
  • Chocolate chips 

How to Make Healthy Chocolate Muffins

There is a full recipe card below.

  • Combine wet ingredients: First, whisk the eggs. Then add applesauce, yogurt and maple syrup and whisk to combine.
  • Add dry ingredients: Add cacao powder, baking powder, baking soda and salt. Whisk thoroughly until smooth and no lumps. This step eliminates the need for 2 bowls with dry and wet ingredients, just like it works with chocolate zucchini bread. It does work if you mix well!

You will see the chocolate mixture rising and bubbling due to the chemical reaction between the acid in the applesauce and baking soda. Don’t worry!how to make healthy chocolate muffins

  • Add flour: Gently mix with spatula just enough to combine. Do not over mix, let batter sit for a few seconds, then stir again. Add chocolate chips and give a few gentle stirs to incorporate.
  • Bake for 25 minutes: Distribute batter evenly between 12 openings of a muffin tin. Bake at 350 degrees on the third or fourth rack from the bottom (farther away from heat). This way the muffins will rise slower, forming a nice dome.how to make healthy chocolate muffins recipe

Storing and Freezing

Storing: Muffins stay fresh for up to one week in the fridge. The way these whole wheat chocolate muffins disappear in my house, I always bake a double batch. Always!

Freezing: If you make a double batch (or if you have any leftover muffins), you can always freeze these little breads. They will last for up to 3 months in any air tight container.

More Healthy Chocolate Recipes

Healthy chocolate muffins in a tin cooling off

Healthy Chocolate Muffins

Healthy Chocolate Muffins

Healthy Chocolate Muffins with Greek yogurt, applesauce, whole wheat flour, cacao powder and honey. Kids absolutely love these fudgy and nutritious muffins.
5 from 24 votes
Print Save Rate
Course: Dessert
Cuisine: North American
Prep Time: 5 minutes
Cook Time: 25 minutes
Total Time: 30 minutes
Servings: 12 muffins
Calories: 173kcal
Author: Olena Osipov

Ingredients

  • 2 large eggs
  • 1 cup applesauce unsweetened
  • 1/2 cup Greek or regular 2%+ fat yogurt, plain
  • 1/2 cup + 2 tbsp maple syrup or honey
  • 1/3 cup cacao or cocoa powder
  • 2 tsp baking powder aluminum free
  • 1 tsp baking soda
  • 1/4 tsp salt
  • 1 3/4 cups whole wheat or spelt flour
  • 1/2 cup chocolate chips
  • Cooking spray I use Misto

Instructions

  • Preheat oven to 350 degrees F and spray silicone muffin tin with cooking spray. Set aside.
  • In a medium mixing bowl, whisk eggs for 15 seconds. Add applesauce, yogurt, maple syrup and whisk to combine. Add cacao powder, baking powder, baking soda, and salt; whisk thoroughly until smooth and no lumps.
    Healthy Chocolate Muffins
  • Add flour and gently mix with spatula just enough to combine. Do not over mix, let batter sit for a few seconds, then stir again. Add chocolate chips and give a few gentle stirs to incorporate.
    Healthy Chocolate Muffins
  • Distribute batter evenly between 12 openings of a tin (I used regular ice cream scoop) and bake on a third-fourth rack from the bottom (farther away from heat) for 25 minutes or until a toothpick inserted in the centre comes out clean.
  • Let muffins cool for about 5 minutes and transfer to a cooling rack to cool off completely.
    Healthy Chocolate Muffins

Store: Refrigerate in an airtight container for up to 1 week or freeze for up to 3 months.

    Notes

    • Applesauce and Greek yogurt: You do need to use both and one cannot be substituted for another. 
    • Maple syrup or honey: Baking is a science and unfortunately you can’t substitute wet sweetener with powdered as it will offset liquid:dry ingredients ratio and recipe will not turn out.
    • Whole wheat flour or spelt flour: Chocolate muffin recipe will not work with any other flour because again "baking is a science".
    • Egg replacement: One time I ran out of eggs and used 1 large egg + 3 tbsp ground flaxseed soaked in 6 tbsp warm water for 10 mins. Which makes a vegan egg replacer. Very moist and fudgy results - try that.

    Nutrition

    Serving: 1muffin | Calories: 173kcal | Carbohydrates: 33g | Protein: 5g | Fat: 4g | Saturated Fat: 3g | Cholesterol: 28mg | Sodium: 258mg | Potassium: 192mg | Fiber: 3g | Sugar: 16g | Vitamin A: 45IU | Vitamin C: 1mg | Calcium: 91mg | Iron: 1mg
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