Chocolate Chip Greek Yogurt Muffins
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.

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!

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.


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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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.

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.

More muffins recipes you will love!
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Chocolate Chip Greek Yogurt Muffins
by: claire cary
Equipment
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
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
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