These healthy chocolate muffins are perfect for breakfast or snack time. Made with Greek yogurt, they’re lower in added sugar and full of flavor.

Hi friends!
If you’ve been around a while, you know that we eat a lot of muffins. These Healthy Chocolate Muffins are the newest addition to our lineup and a favorite of my youngest kiddo.
He’s recently decided he no longer likes bananas so that knocks out a lot of muffin choices. Luckily, he is still a fan of chocolate and he loves my Healthy Black Bean Bars and my Chocolate Pea Cookies.
But he’s a growing boy and in my quest to always have healthy snacks on hand, I did some testing to make a banana-free chocolate muffin he will eat.
Healthy Banana Muffin Recipes
If you’re new here, the rest of the family enjoys bananas. Here are some of our other favorite muffins that do include bananas:
Healthy Chocolate Chip Pumpkin Muffins
And if you happen to be in the mood for pumpkin instead of chocolate, check out these favorites:
- Easy Pumpkin Bread with Chocolate Chips (can be made as muffins)
- Chocolate Chip Pumpkin Bars with Quinoa
- Pumpkin Yogurt Bars

Healthy Chocolate Muffin Ingredients
The ingredients for these muffins are super simple and you probably have most of them on hand already! You’ll need:
- Plain Greek yogurt – adds protein and helps keep the muffins moist
- Eggs – for structure
- Applesauce and sugar – to add sweetness
- Oil – I use avocado oil but any mild oil is fine
- Milk – Dairy or non-dairy will work
- Flour – I like to use white whole wheat flour, but all-purpose is fine
- Cocoa powder- look for unsweetened!
- Baking powder and baking soda – to help them rise!
- Chocolate chips – mix them in or just add them to the top. Or skip them all together.
How To Make Healthy Chocolate Muffins
These muffins can be made in one bowl for easy cleanup:
- In a large mixing bowl, combine yogurt, eggs, applesauce, sugar and milk and mix well.
- Add dry ingredients and stir until just combined.
- Scoop into silicone or lined muffin tins and bake!

Healthy Chocolate Muffin Recipe
PrintHealthy Chocolate Muffins
These healthy chocolate muffins are perfect for breakfast or snack time. Made with Greek yogurt, they’re lower in added sugar and full of flavor.
- Yield: makes 12 muffins 1x
Ingredients
- 3/4 cup plain Greek yogurt
- 2 eggs
- 1/3 cup oil
- 1/3 cup milk
- 1/3 cup applesauce
- 1/3 cup sugar
- 1.5 cups flour (i use white whole wheat flour)
- 1/3 cup unsweetened cocoa powder
- 1 tsp baking soda
- 1 tsp baking powder
- pinch of salt
- 1/3 cup chocolate chips
Instructions
- Preheat oven to 375 degrees F.
- Mix yogurt, eggs, oil, milk, applesauce and sugar in a large mixing bowl.
- Add remaining ingredients and stir until just combined.
- Spoon into silicone or lined muffin tins and bake for 16 minutes or until a toothpick inserted comes out clean.
Healthy Chocolate Muffins FAQs
How to store healthy chocolate muffins?
Store in a container or bag on the counter for 2-3 days. If you have any left, move them to the fridge to help them last longer.
Can you freeze chocolate muffins?
Yes! Let them cool completely, then store in a freezer safe bag. When ready to eat, thaw in the microwave or on the counter.
Can I use regular yogurt?
Yes. If you don’t have Greek yogurt, regular plain yogurt will work just fine. You can also sub in vanilla yogurt.
Can I make gluten-free healthy chocolate muffins?
To make these gluten-free, swap a 1:1 gf flour mix for the flour. I like King Arthur Gluten-Free Measure for Measure.
Healthy Chocolate Muffins

Healthy Muffin Recipes
Need more muffins and bars to try?
- Best Ever Double Chocolate Muffins
- Moist Chocolate Muffins
- Apple Cinnamon Red Lentil Muffins
- Blondie Snickerdoodle Bars
- Sweet Potato White Bean Bars
Enjoy!
–Lindsay–
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These are so good! I would like to know how many calories per muffin though because I’m on a diet. Perfect texture though, and not too overly sweet like many muffin recipes. Just right!
My kids loved these! Any idea on how to get these not to stick to paper muffin liners?
i don’t have any suggestions, sorry! I use a silicone muffin tin to bake them.