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Healthy Chocolate Muffins

February 5, 2025 by Lindsay 6 Comments

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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.

healthy chocolate muffins with Greek yogurt

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:

  • Banana Flax Muffins
  • Lentil Banana Muffins
  • Sweet Potato Banana Bites
  • Banana Carrot Muffins

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 recipe

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!

greek yogurt chocolate muffins

Healthy Chocolate Muffin Recipe

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Healthy Chocolate Muffins

healthy chocolate muffins
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5 from 2 reviews

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.

  • Author: Lindsay
  • Yield: makes 12 muffins 1x

Ingredients

Scale
  • 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

  1. Preheat oven to 375 degrees F.
  2. Mix yogurt, eggs, oil, milk, applesauce and sugar in a large mixing bowl.
  3. Add remaining ingredients and stir until just combined.
  4. Spoon into silicone or lined muffin tins and bake for 16 minutes or until a toothpick inserted comes out clean.

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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

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.

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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Filed Under: Baking, Breakfast, Healthy Muffins & Bars, Snack Tagged With: Chocolate Chips, Cocoa Powder, Egg, Milk, Oil, Yogurt

About Lindsay

Lindsay Livingston is a Registered Dietitian and new mom from Columbus, Ohio. On her blog, she shares simple, healthy recipes, nutrition tips, workouts and snapshots of her life. Follow her on Twitter @LeanGrnBeanBlog and Instagram @TheLeanGreenBean and be sure to subscribe via RSS or email so you never miss a post!

Reader Interactions

Comments

  1. Stephanie says

    February 14, 2025 at 2:17 PM

    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!

    Reply
  2. Kim says

    March 2, 2025 at 4:01 PM

    My kids loved these! Any idea on how to get these not to stick to paper muffin liners?

    Reply
    • Lindsay says

      March 5, 2025 at 8:26 AM

      i don’t have any suggestions, sorry! I use a silicone muffin tin to bake them.

      Reply
  3. Wendy says

    April 1, 2025 at 5:46 PM

    These were so easy to make and my kids loved when I surprised them with the muffins for after school snack. They told me over and over how YUMMY they are. Thanks Lindsay!

    Reply
  4. Kristin says

    April 3, 2025 at 11:34 AM

    Have you tried eliminating the oil and adding more eggs or applesauce? They are delicious!

    Reply
    • Lindsay says

      April 3, 2025 at 1:11 PM

      you could definitely try replacing the oil with applesauce

      Reply

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Lindsay Livingston The Lean Green Bean Healthy Living Tips and Tricks

I'm a Registered Dietitian and mom of three from Columbus, Ohio. I use this blog to share simple, healthy recipes, nutrition tips, and an honest glimpse of motherhood!

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Questions? Comments? Email me: [email protected]

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