These irresistible Skinny Chocolate Muffins prove that healthy can be absolutely delicious. At just 153 calories per serving, these moist, chocolatey treats are perfect for guilt-free indulgence. Packed with 5g of protein and 2g of fiber, they’re the ideal breakfast option or afternoon pick-me-up. Ready in just 25 minutes, you’ll love how these better-for-you muffins satisfy your sweet cravings while keeping your wellness goals on track.
Essential Ingredients

- Flours: 1/2 cup whole wheat + 2/3 cup all-purpose for perfect texture balance
- Sweetener: 1/3 cup granulated sugar (just enough for balanced sweetness)
- Cocoa & Chips: 1/3 cup unsweetened cocoa powder + 1/2 cup mini chocolate chips for rich chocolate flavor
- Leavening: 1 teaspoon baking soda + 1/4 teaspoon cinnamon & salt for perfect rise
- Wet Ingredients: 2 eggs, 1/2 cup Greek yogurt, 1/2 cup milk for moisture
- Moisture Boost: 1/4 cup applesauce (or oil/mashed banana) + 1 teaspoon vanilla for tender crumb
Step-by-Step Instructions
- Prep Work: Heat oven to 350°F and grease standard muffin tin for perfect release
- Dry Mixture: Combine flours, sugar, cocoa, baking soda, cinnamon, salt, and chips in large bowl
- Wet Mixture: Beat eggs, yogurt, milk, applesauce, and vanilla until smooth
- Combining: Create well in dry ingredients, add wet mixture, stir just until combined
- Baking Magic: Fill muffin cups evenly, bake 12-15 minutes until toothpick comes clean
- Finishing Touch: Cool completely on wire rack for best texture
Variations & Substitutions
These muffins are super flexible! You can swap the applesauce with mashed banana or oil based on what you have. For a dairy-free version, use almond milk and dairy-free yogurt. Want them extra rich? Replace the Greek yogurt with sour cream. To make them even healthier, try using all whole wheat flour – just know they might be a bit denser.
Storage Tips
Your chocolate muffins will stay fresh at room temperature for 3-4 days in an airtight container. Pop them in the fridge to keep them good for up to a week! They also freeze really well – just put them in a freezer bag and they’ll last about 3 months. When you want one, let it thaw at room temperature or warm it in the microwave for 20-30 seconds.
Serving Suggestions
These muffins are amazing slightly warm! Try splitting one open and adding a small pat of butter that gets all melty. They’re perfect for breakfast with a cup of coffee or milk, or as an afternoon snack. Pack them in lunch boxes or serve them at brunch. For a special treat, warm them up and top with a tiny scoop of vanilla ice cream!

Skinny Chocolate Muffins
Equipment
- 12-cup muffin tin
- Large mixing bowl
- Medium mixing bowl
- Wire rack
Ingredients
Dry Ingredients
- 1/2 cup whole wheat flour
- 2/3 cup all-purpose flour
- 1/3 cup granulated sugar
- 1/3 cup unsweetened cocoa powder
- 1 teaspoon baking soda
- 1/4 teaspoon ground cinnamon
- 1/4 teaspoon salt
- 1/2 cup mini semi-sweet chocolate chips
Wet Ingredients
- 2 large eggs
- 1/2 cup Greek yogurt or sour cream
- 1/2 cup milk
- 1/4 cup applesauce oil or mashed banana can be substituted
- 1 teaspoon vanilla extract
Instructions
- Preheat oven to 350 degrees F. Grease a standard 12 cup muffin tin with non-stick cooking spray.
- In a large bowl, combine the dry ingredients: flours, sugar, cocoa, baking soda, cinnamon, salt and chocolate chips and stir to combine.
- In a medium bowl, beat together the eggs, yogurt, milk, applesauce and vanilla.
- Make a well in the center of the dry ingredients and stir in the wet mixture, stirring just until moistened (don’t over-mix).
- Divide batter between muffin cups. Bake for 12-15 minutes or until a toothpick inserted in the center comes out clean.
- Remove to a wire rack to cool completely.