Greek Yogurt Muffins
Published Nov 04, 2026
Greek yogurt muffins made with whole milk Greek yogurt and chocolate chips. This recipe makes 12 muffins, and they're freezer-friendly.
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I really like using Greek yogurt instead of milk when I make muffins, but I still keep the butter in there too. I know a lot of people use yogurt to replace butter in baking, but I’ve always liked using both. I’ve been baking with Stonyfield Organic Whole Milk Greek Yogurt for years (over 6+ to be exact!), and I use a full cup of it in these Greek yogurt muffins. The batter does get pretty thick, definitely thicker than if I’d used milk. That’s totally normal, so don’t stress it.
Recipe Testing Notes
For the past 10 years, I’ve tested every recipe before sharing it with you! These notes give you a peek into the process of developing this Greek Yogurt Muffins recipe.
When I was working on these Greek yogurt muffins, I already knew I wanted to use Stonyfield Organic Whole Milk Greek Yogurt. It’s my tried-and-true brand of Greek yogurt, so that wasn’t really something I needed to experiment with. What I did have to play around with was how much to use, since I was taking out the milk but keeping the melted butter. I ended up using a full cup, and I liked the moisture I got from that.
I also try not to mess with the batter too much once the flour goes in. I mix until everything is combined, fold in the chocolate chips, and that’s it.
Happy Cooking!
– Yumna
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Greek Yogurt Muffins Ingredients
- Greek yogurt: Stonyfield Organic Whole Milk Greek Yogurt. It’s made with 100% organic milk from pasture-raised cows, and I like using the whole milk version for baking because it’s thick and creamy. Regular yogurt is thinner and can change the consistency of the batter, so I’d stick with Greek yogurt here.
- Dry ingredients: All-purpose flour, baking powder, baking soda, and salt. I spoon the flour into my measuring cup and level it off rather than scooping directly from the bag. Too much flour can make the muffins dense.
- Wet ingredients: Granulated sugar, eggs, melted butter, and vanilla extract. I let the melted butter cool slightly before mixing it with the eggs so it doesn’t start cooking them.
- Chocolate chips: I use semi-sweet chocolate chips, but mini chocolate chips work too. The same 1 cup will give a more even distribution throughout the muffins.
How to Make Greek Yogurt Muffins
These step-by-step photos walk you through how to make Greek Yogurt Muffins. For the full ingredient list and detailed instructions, head to the recipe card below, or skip straight to the → Greek Yogurt Muffins below
1. Whisk the Eggs and Sugar
Start with the eggs and sugar in a large bowl, whisking until the mixture looks smooth.
2. Add the Greek Yogurt
Add in the yogurt, cooled melted butter, and vanilla extract. Whisk everything together until evenly combined.
3. Add the Dry Ingredients
Switch to a spatula and gently mix the flour mixture into the wet ingredients until no dry patches remain.
4. Fold the Chocolate Chips
The batter should look thick and scoopable, with the chocolate chips evenly distributed throughout.
5. Fill the Muffin Pan
Spoon the batter into the lined muffin cups, filling each one almost to the top.
6. Bake the Muffins
The tops should be lightly golden, and a toothpick inserted into the center should come out clean or with a few moist crumbs. Let them cool briefly in the pan before transferring to a wire rack.
Full Greek Yogurt Muffins Recipe
Greek Yogurt Muffin Recipe
Ingredients
- 2 cups all-purpose flour
- 2 teaspoons baking powder
- ½ teaspoon baking soda
- ½ teaspoon salt
- ¾ cup granulated sugar
- 2 large eggs
- 1 cup Stonyfield Whole Milk Greek yogurt
- ½ cup unsalted butter melted and cooled slightly
- 2 teaspoons vanilla extract
- 1 cup semi-sweet chocolate chips
Instructions
- Preheat the oven to 375°F. Line a 12-cup muffin pan with muffin liners.
- In a medium bowl, whisk together the flour, baking powder, baking soda, and salt.
- In a large bowl, whisk together the sugar and eggs until smooth. Add the Greek yogurt, melted butter, and vanilla and whisk until well combined.
- Add the dry ingredients to the wet ingredients and use a spatula to mix just until combined. Fold in the chocolate chips. The batter should be thick and scoopable.
- Divide the batter evenly among the muffin cups, filling them almost to the top.
- Bake for 22-25 minutes, or until a toothpick inserted in the center comes out clean or with a few moist crumbs.
- Cool in the pan for 5 minutes, then transfer to a wire rack.
Equipment
Notes
Nutrition
Nutrition information provided is an estimate. It will vary based on cooking method and specific ingredients used.
Recipe Variations
- Make lemon blueberry muffins. Swap the chocolate chips for 1 cup of fresh blueberries and add 1 teaspoon of lemon zest to the wet ingredients.
- Add cinnamon sugar tops. Mix 2 tablespoons of granulated sugar with ½ teaspoon of ground cinnamon and sprinkle it evenly over the muffins before baking.
- Add some nuts. Replace ½ cup of the chocolate chips with ½ cup of chopped walnuts or pecans. I like this option when I want a little crunch along with the chocolate.
Recipe Tips
- Use an ice cream scoop to portion the batter. I find this so much easier than using two spoons, especially with a thicker muffin batter. It also helps keep the muffins about the same size so they bake evenly.
- Keep the oven door closed until near the end of baking. Opening the door too early drops the oven temperature and can cause the muffins to sink before they’ve finished rising.
- Let the muffins cool before removing the liners. I know it’s tempting to eat one right away, but warm muffins can stick to the paper. The liners should peel away more easily once they’ve cooled.
Troubleshooting
It’s supposed to be thick! The Greek yogurt makes this batter thicker than a traditional muffin batter, but it should still be soft enough to scoop into the muffin pan. I wouldn’t add milk or water to thin it out.
The two things I’d check first are the flour measurement and baking time. Too much flour can make the muffins dry, and leaving them in the oven too long can do the same. I start checking toward the lower end of the baking time, especially if my oven tends to run hot.
