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Meal Type ยป Gluten Free Snacks ยป Chocolate Chip Greek Yogurt Muffins

Chocolate Chip Greek Yogurt Muffins

Claire Cary

By

Claire Cary

No ratings yet
May 19, 2026
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If you’re looking for a higher protein sweet treat, look no further than these fluffy greek yogurt muffins. They’re made in one bowl, perfectly sweet, gluten free, moist, tender and can be made with blueberries or chocolate chips.

two greek yogurt muffins stacked on each other to show texture

Sometimes you want a sweet treat that is made with better for you ingredients but doesn’t taste like it’s made with better for you ingredients. Enter: these greek yogurt muffins! They’re a higher protein recipe (6-7 grams per muffin) but without any added protein powder. Enjoy them plain, with chocolate chips, blueberries or a combination of the two!

I love having these for a healthier dessert, but they make for a great grab and go breakfast (with a strawberry protein shake!) or after school snack for the kids.

Tips before we bake!

  • I suggest a full fat greek yogurt for the best texture- it will make them SO moist, but if you only have a lower fat option that is totally fine.
  • Be sure to let the muffins cool completely. If you try to eat them fresh out of the oven, the texture will not be set and the muffin may stick to the wrapper a bit. While not necessary, you can swap the liners with a bit of oil spray before adding the batter to really ensure they won’t stick.
  • I sprinkled a bit of sanding sugar on top of my muffins which adds a really nice crunch to the final product. This is totally optional!
ingredients in bowls with labels

How to make greek yogurt muffins

Preheat oven to 425 degrees Fahrenhit. Line a 12 cavity muffin tin with liners and set aside.

In a medium mixing bowl, whisk together the melted butter and sugar. Whisk in the remaining wet ingredients until smooth.

Whisk in the dry ingredients (aside from the chocolate chips) making sure to spoon and level the flour to measure. The batter will be very thick! Fold in the chocolate chips.

wet ingredients whisked in a glass bowl
batter in a glass bowl

Let the batter rest for about 10 minutes- this will help the muffins get really fluffy when they bake. After 10 minutes, scoop into the muffin tin, filling each all the way up so they grow nice and tall.

Bake at 425 for 5 minutes, then reduce the heat to 350 and bake an additional 14-17 minutes or until a toothpick comes out clean. Let cool before serving to ensure the wrapper and muffin pull apart easily. Enjoy and try my banana protein muffins next!

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batter in the tin before going in the oven with sugar on top

Tips for fluffy muffins

Keep the batter thick. The batter for these greek yogurt muffins should be quite thick. This will help the tops stay nice and round. When you scoop the batter into the muffin tray, it should hold it shape and stay rounded on top and not spread out.

Fill the muffins to the top. Most recipes will tell you to fill cupcakes/muffins about 3/4 of the way up, but with this recipe, you want to fill it all the way to the brim so they can rise nice and tall.

Start at a higher temperature. One trick that I like to use with muffins is to bake at a higher temperature for about 5 minutes, then lower to 350 for the remaining time. For this recipe, I would suggest baking at 425 Fahrenheit for 5 minutes, then lower the temperature to 350 and bake an additional 15 or so minutes.

bite taken out of the greek yogurt muffin with chocolate chips

How to store and freeze

Store these greek yogurt muffins at room temperature in a sealed container. I like to microwave them for a few seconds before eating if they’ve been sitting around for a bit so the chocolate gets nice and melty again. They should keep for about 3 days at room temperature or up to 5 in the fridge.

You can also freeze these! Just let them cool completely, then transfer to a freezer safe bag. Freeze for up to 2 months, then reheat in the oven at 300 just until warm through the center. I like to freeze them without the wrapper on.

greek yogurt muffin cut in half to show fluffy texture

More muffins recipes you will love!

  • Gluten Free Strawberry Muffins
  • Matcha Muffins
  • Sweet Potato Muffins

Be sure to follow along on on instagram and subscribe to my email list for more recipes and updates. Leave a comment and rating below if you try this recipe and let us know how it turns out!

No ratings yet

Chocolate Chip Greek Yogurt Muffins

by: claire cary

If you’re looking for a higher protein sweet treat, look no further than these fluffy greek yogurt muffins. They’re made in one bowl, perfectly sweet, gluten free, moist, tender and can be made with blueberries or chocolate chips.
/ /
Prep: 15 minutes mins
Cook: 20 minutes mins
Total: 35 minutes mins
12

Equipment

  • Muffin tin
  • Muffin liners

Ingredients

Wet

  • ⅓ cup unsalted butter melted then cooled
  • ⅔ cup white sugar
  • 2 eggs
  • 1 ¼ cup plain full fat greek yogurt
  • 2 teaspoons vanilla extract

Dry

  • 2 cups gluten free all purpose baking flour
  • 2 ¼ teaspoons baking powder
  • ¼ teaspoon baking soda
  • ½ teaspoon salt
  • ½ teaspoon cinnamon
  • 1 cup chocolate chips
US Customary – Metric

Instructions

  • Preheat oven to 425 degrees Fahrenhit.
  • Line a 12 cavity muffin tin with liners and set aside.
  • In a medium mixing bowl, whisk together the melted butter and sugar. Whisk in the remaining wet ingredients until smooth.
  • Whisk in the dry ingredients (aside from the chocolate chips) making sure to spoon and level the flour to measure. The batter will be very thick! Fold in the chocolate chips.
  • Let the batter rest for about 10 minutes- this will help the muffins get really fluffy when they bake.
  • After 10 minutes, scoop into the muffin tin, filling each all the way up so they grow nice and tall.
  • Bake at 425 for 5 minutes, then reduce the heat to 350 and bake an additional 14-17 minutes or until a toothpick comes out clean.
  • Let cool before serving or the muffin will get stuck to the wrapper. Enjoy!

Notes

Feel free to swap the chocolate chips for blueberries if you prefer!
Serving: 1muffin / Calories: 256kcal / Carbohydrates: 37g / Protein: 7g / Fat: 10g / Saturated Fat: 6g / Polyunsaturated Fat: 0.4g / Monounsaturated Fat: 2g / Trans Fat: 0.2g / Cholesterol: 44mg / Sodium: 228mg / Potassium: 43mg / Fiber: 2g / Sugar: 22g / Vitamin A: 232IU / Vitamin C: 0.1mg / Calcium: 105mg / Iron: 1mg

Did you make this?

Mention @eatwithclarity or tag #eatwithclarity!

Related posts:

  1. Brownie Batter Chocolate Hummus
  2. Chocolate Chip Protein Cookies
  3. Blueberry Protein Donuts
  4. Blueberry Protein Muffins

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claire cary

Welcome,
I’m Claire

Eat With Clarity is a place for gluten free recipes that are just as good as the real thing. With plenty of vegan, vegetarian and paleo options, there is something here for everyone!


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