Healthy Chocolate Mini Muffins
Updated Jan 09, 2026
These easy Healthy Chocolate Mini Muffins are great for kids! They’re made with greek yogurt and have double the chocolate flavor.
⭐️Review⭐️
“Muffins turned out perfect. My whole family enjoyed them” -Lisa
Mini muffins are by far the most requested snack from my kids. They never last long in our house and are always a snack I can count on them eating!
I’m not sure if it’s the mini adorable size, but my kids will eat these up and request 2-4 muffins each in for a snack. They are the perfect lunchbox size and easy to keep on hand for a snack or something for your sweet tooth!
Since they love mini muffins so much, I always try to sneak in a little nutrition into them where I can. In this case, that’s greek yogurt! It’s a great way to make muffins moist and add a little protein too.
My boys will eat mini muffins of all kinds and I’ll share a few more recipes they love at the bottom of this post.
Ingredients & Notes
The full recipe and instructions are located at the bottom of this post, but here is what you will need to make these muffins.
- Whole milk greek yogurt: the unsweetened kind
- Unsalted butter
- Eggs
- All-purpose flour
- Cocoa powder: or substitute raw cacao powder
- Maple syrup: the real stuff. This is one my favorite natural sweetener to bake with.
- Vanilla extract
- Salt: just a little bit to make the flavors pop.
- Baking powder & baking soda: our leavening agents.
- Mini semi sweet chocolate chips: mini chips mean there’s chocolate in every bite!
How to make healthy chocolate mini muffins
You can find the full printable recipe with the instructions at the bottom of this post, but here’s the photo step by step.
Step 1: Whisk together the flour, salt, cocoa powder, baking soda, and baking powder in a mixing bowl until combined.
Step 2: In a separate bowl, whisk together the greek yogurt, vanilla extract, melted butter, and maple syrup. Whisk in the eggs.
Step 3: Add the dry ingredients to the wet and mix until just combined using a rubber spatula. Do not over mix the batter.
Step 4: Fold the mini chocolate chips into the muffin batter.
Step 5: Spray a mini muffin tin with nonstick spray. Distribute the batter into the pan, filling each mini muffin tin ¾ of the way full.
Recipe Note
This will make 1 and a half tins full of mini muffins, you will not use all the batter for one muffin tin. This recipe yields 36 mini muffins in total.
Step 6: Bake the healthy chocolate mini muffins at 350 degrees for 12-14 minutes, until a toothpick inserted comes out clean.
Cool the muffins for 2-3 minutes in the pan, then remove them onto a wire cooling rack to cool completely.
Storing
Store leftover mini muffins in an airtight container in the refrigerator for 3-4 days.
More Snack Recipes
- Pancake Mini Muffins
- ABC Mini Muffins
- Greek Yogurt Banana Bread
- Birthday Cake Mini Muffins
- Oatmeal Cookie Mini Muffins
- Greek Yogurt Snack Cake
- Greek Yogurt Banana Muffins
- Pumpkin Donut Mini Muffins
- Greek Yogurt Chocolate Chip Muffins
- Chocolate Snack Cake
- Greek Yogurt Banana Mini Muffins
- Blueberry Mini Muffins
- Banana Mini Muffins
- Pumpkin Mini Muffins
- Chocolate Chip Mini Muffins
Healthy Chocolate Mini Muffins
Ingredients
- 1 cup plain whole milk unsweetened greek yogurt
- ⅓ cup unsalted butter, melted and slightly cooled
- 2 eggs
- 1 cup all-purpose flour
- ⅓ cup cocoa powder
- ½ cup maple syrup
- 1 tablespoon vanilla extract
- ¼ teaspoon salt
- 1 teaspoon baking powder
- ¼ teaspoon baking soda
- 1 cup mini semi sweet chocolate chips
Instructions
- Whisk together the flour, cocoa powder, salt, baking soda, and baking powder in a mixing bowl until combined.
- In a separate bowl, whisk together the greek yogurt, vanilla extract, melted butter, and maple syrup.
- Whisk the eggs into the other wet ingredients.
- Add the dry ingredients to the wet and mix until just combined using a rubber spatula. Do not over mix the batter.
- Fold in the mini chocolate chips using the rubber spatula.
- Spray a mini muffin tin with nonstick spray.
- Distribute the batter into the pan, filling each mini muffin tin ¾ of the way full. The easiest way to do this is by using a mini cookie scoop. Note – this will make 1 and a half tins full of muffins, you will not use all the batter for one muffin tin. It will yield 36 mini muffins in total
- Bake the mini muffins at 350°F for 12-14 minutes, until a toothpick inserted comes out clean
- Cool the mini muffins 2-3 minutes in the pan, then remove them onto a wire cooling rack to cool completely
BEST chocolate muffin recipe ever! love that it didn’t need oil. I did have to substitute sour cream and they came out perfect. 100% toddler approved! thank you so much!!
So glad you enjoyed the recipe Venessa!
What if you don’t have cocoa powder?
I don’t have a substitute for that unfortunately. You really need it for the right flavor in this recipe
How long for regular sized muffins ?!
I would start with 18-22 minutes, then just do a toothpick test from there until it comes out clean!