Greek Yogurt Chocolate Chip Muffins
Updated Nov 11, 2025
These Greek Yogurt Muffins are light and fluffy, sweetened naturally with pure maple syrup, and a great way to add more protein to your day!
Greek Yogurt Muffins Are So Delicious!
Light and fluffy muffins are the best kind of muffins, and my secret for that perfect airy texture is using greek yogurt.
My boys love these chocolate chip muffins and you would never guess that they are made with healthier ingredients. We make them full size bakery style and also in mini chocolate chip muffin size.
I had a reader ask me if this muffin could be made in a cake pan and you know I had to try it! If you want this recipe but in cake squares, check out this Greek Yogurt Snack Cake recipe.
Who doesn’t love chocolate chip muffins for breakfast? Greek yogurt chocolate chip muffins are the ultimate breakfast muffin that combines flavor and nutrition for a wholesome yet still delicious treat!
These greek yogurt muffins have become such a favorite in our house that I went on to also make these mini blueberry muffins using similar ingredients.
Ingredients & Notes
The full ingredient amounts and instructions can be found at the bottom of the post in the recipe card, but here’s what you’ll need to make these.
- Greek yogurt: the plain whole milk unsweetened version. You can also use fat free plain yogurt if you want to.
- Coconut oil: measure it while solid, then melt it.
- Eggs
- Vanilla extract
- Salt
- Baking powder & baking soda
- Real maple syrup: not pancake syrup.
- Flour: you can use whole wheat pastry flour or all-purpose flour.
- Mini chocolate chips: semi-sweet or dark chocolate.
How to make chocolate chip muffins with greek yogurt
Step one: Whisk together the dry ingredients in a mixing bowl: flour, baking powder, baking soda, and salt.
Step two: In a separate mixing bowl, whisk together the wet ingredients: greek yogurt, maple syrup, eggs, vanilla, and melted coconut oil.
Step three: Add the dry ingredients to the wet, and mix together with a rubber spatula until just combined. Do not over mix, as this will result in dense muffins.
Step four: Reserve a few spoonfuls of chocolate chips to top the muffins, and fold the rest into the batter using a rubber spatula.
Step five: Line a muffin tin with parchment paper muffin liners and distribute the batter evenly into the 12 cups.
Joy’s Tip
I use parchment paper muffins every time I make muffins, as they won’t stick to the wrapper at all! If you don’t use liners, use cooking spray first to the muffin tin before adding the batter.
Step six: Sprinkle the tops of the muffins with additional mini chocolate chips.
Step seven: Bake the muffins at 350 degrees for around 20 minutes, or until a toothpick inserted comes out clean.
Oh my gosh! These are by far the best muffins I’ve ever made. My husband said they tasted like chocolate chip cookies. I had to intervene because he would have ate half the pan hahaha! My kids also loved them.
Can you freeze them?
Yes! One of my favorite things is to have extra muffins in the freezer. These can be stored in an airtight container or bag in the freezer for 2-3 months.
Simply pop one out and microwave it for 20-30 seconds for a quick and yummy breakfast or snack.
More recipes
- The Best Gluten Free Chocolate Muffins
- Pancake Muffins
- Greek Yogurt Pumpkin Bread
- Greek Yogurt Chocolate Chip Bread
- Carrot Cake Snack Bars
- Greek Yogurt Banana Bread
- Wholesome Banana Muffins
- Greek Yogurt Banana Mini Muffins
- Bakery Style Chocolate Chip Muffins
- Double Chocolate Muffins
- Banana Mini Muffins
- Greek Yogurt Chocolate Banana Muffins
How to store
Greek yogurt muffins can be stored in an airtight bag or container in the refrigerator for 4-5 days, or in the freezer for 2-3 months.
Greek Yogurt Chocolate Chip Muffins
Ingredients
- 1 cup plain whole fat greek yogurt
- 1/4 cup coconut oil, melted
- 2 eggs
- 1 tablespoon vanilla extract
- 1/4 teaspoon salt
- 1 teaspoon baking powder
- 1/2 teaspoon baking soda
- 1/2 cup real maple syrup
- 1 1/2 cups whole wheat pastry flour , or all purpose flour
- 1 cup mini semi sweet chocolate chips
Instructions
- In a mixing bowl, whisk together the dry ingredients: flour, salt, baking soda, and baking powder.
- In a separate mixing bowl, whisk together the wet ingredients: greek yogurt, maple syrup, eggs, vanilla, and melted coconut oil.
- Add the dry ingredients to the wet, and mix it all together with a rubber spatula until just combined (be careful not to over mix).
- Reserve a few spoonfuls of chocolate chips to top the muffins, and fold the rest into the batter.
- Line a muffin tin with parchment paper muffin liners, or use cooking spray for regular liners or no liners.
- Divide the muffin batter into the 12 cups, then top with the reserved chocolate chips.
- Bake the chocolate chip muffins at 350 degrees for 18 – 22 minutes, or until a toothpick inserted comes out clean
Notes
Tips for light and fluffy texture
Be sure not to over mix the batter, as this will result in too dense muffins. The key is to mix until just combined, the same goes when you add in the chocolate chips.How do I measure the coconut oil?
Measure the coconut oil while solid, then melt in the microwave for 15 – 45 seconds until it turns to liquid.Can I freeze these muffins?
Yes! Simply allow the muffins to cool, then store in a ziploc bag in your freezer. Once you are ready to eat one, microwave it for 15 – 30 seconds, or until heated through.Can I use a different flour?
Yes! You can substitute whole wheat pastry flour for all-purpose flour.Nutrition
Delicious !!! One of the best muffins .. actually THE best!
These are so good! My kids love them!
I’m struggling to figure out how you determined there was 9 gm of protein per muffin? What am I missing? Based on these ingredients I’m guessing 3 gm protein max per muffin.
The nutritional information is automatically calculated based on the original recipe. Using other types of ingredients or substitutions can alter the nutritional content.
could you add vanilla protein powder to the mix?
Hi! Just wondering, can I substitute anything else for coconut oil, such as apple sauce or butter?
Yes! I have used melted butter (an equal amount) and it works very well!
@Joy Shull,
Can you use olive oil? 🙂
@Shannen, I wouldn’t use olive oil because it might have a weird taste. You can use butter, applesauce, etc… you can also look up substitutes to coconut oil if you want more ideas! Hope this helps
Instead of making these as a muffin, can I mix them up and bake them as cookies?
Would they bake just the same? If so about how long would I cook them?
Thank you!!
I have not tried it so I am not sure.
These were so simple and taste great!
Oh my gosh! These are by far the best muffins I’ve ever made. My husband said they tasted like chocolate chip cookies. I had to intervene because he would have ate half the pan hahaha! My kids also loved them. Thank you for this delicious, yet healthy muffin recipe. I love that I can sneak some extra nutrition into my kids with these. The Greek yogurt is genius. Also, thank you so much for sharing your creativity and talent with the world. Many of your recipes are on our regular rotation and we’ve yet to try one that we didn’t like. As someone who cooking doesn’t come natural for, your website is a life saver!
Nicole,
thank you so much for the lovely comment, you made my day! I’m so very glad you and your family are enjoying the recipes!! 🙂
@Nicole, what a lovely comment.
@joy shull, I can’t wait to make these in the morning for my kids 🙂 thank you.
This is one of the yummiest muffin recipes I’ve ever had. I was looking for a healthy muffin recipe without banana since I ran out of bananas my second week after grocery shopping. I reduced the maple syrup to 1/3 of a cup since my yogurt had sugar in it. I also swapped our the mini chocolate chips for dark chocolate, Very good! Highly recommend!
So glad you enjoyed the recipe Melissa!
These muffins looks so delicious, chocolatey and comforting! Perfect for weekend brunch!