Yogurt Muffins



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Here’s how to make the best yogurt muffins with four different flavor variations. They’re protein-packed, kid-friendly, easy to make and perfect for meal prep.

I love meal prepping some sort of healthy baked good recipe over the weekend to have on hand for breakfast and snacks during the week and these yogurt muffins have been my go-to recently! I’m sharing the simple base recipe along with 4 different mix-in options below.

They’re lightly sweetened with maple syrup, but not overly sweet, so I can feel good about eating one for breakfast. Plus, the Greek yogurt adds some protein, probiotics and calcium and helps to keep these muffins super fluffy and moist.

I’ve already made multiple batches so far and thanks to the different mix-in options I haven’t gotten bored yet! Plus, Olivia is obsessed with them. The strawberry version might just be her favorite!

Photos of 4 different yogurt muffins:

Why You’ll Love These Muffins

  • They’re protein-packed so will keep you full longer.
  • The flavor combinations are endless so you won’t get bored.
  • Great for meal prep and freezer-friendly!
  • They’re portable so you can take them on-the-go.
Ingredients measured out to make yogurt muffins 4 ways: whole wheat pastry flour, cinnamon, Greek yogurt, sea salt, maple syrup, eggs, baking powder, coconut oil, vanilla, almond milk, baking soda, strawberries, apples, blueberries and chocolate chips.

Ingredients Needed

  • whole wheat pastry flour – whole wheat pastry flour is the key to making these yogurt muffins light and fluffy. My go-to brand is Bob’s Red Mill whole wheat pastry flour. If you can’t find whole wheat pastry flour you can also use white whole wheat flour, a blend of all-purpose and regular whole wheat flour or just regular all-purpose flour.
  • baking powder and baking soda – helps the muffins rise.
  • sea salt – balances the flavors of the muffins.
  • cinnamon – a nice warming spice for these muffins.
  • eggs – helps bind the ingredients together and provide structure for the muffins.
  • Greek yogurt – Greek yogurt keeps these muffins moist without a lot of added oil. I recommend using plain whole milk (full fat) yogurt for the best results.
  • coconut oil – helps keep these muffins super moist and fluffy.
  • maple syrup – I love using maple syrup as the natural sweetener in these muffins, but I bet honey or even monk fruit maple syrup would work fine as a substitute.
  • unsweetened almond milk – I used unsweetened vanilla almond milk, but any type of milk will work, including cow’s milk.
  • vanilla extract – a flavor enhancer.
  • mix-ins – fresh blueberries, fresh strawberries, chopped apples or chocolate chips.
Side by side photos of a variety of yogurt muffins in a muffin tin, before and after being baked.

How to Make

Step 1: Preheat the oven to 400ºF. Line a muffin pan with paper or silicone muffin cups.

Step 2: In a large mixing bowl, combine the dry ingredients: flour, baking powder, baking soda, salt and cinnamon.

Step 3: In a medium bowl, whisk together the wet ingredients: eggs, yogurt, oil, maple syrup, almond milk and vanilla extract. Add the wet ingredients to the dry ingredients and stir until just combined. Make sure you don’t over-mix or the muffins will be too dense after baking.

Step 4: Gently fold in mix-in of choice and divide batter evenly into muffin tins.

Step 5: Bake for 18-20 minutes or until a toothpick inserted into the center of the muffin comes out clean. Let the muffins cool for a few minutes in the pan and then let cool completely on a wire rack.


Tips for Success

  • Make sure you’re using room temperature milk, eggs, maple syrup and yogurt! If any of these ingredients are cool, the coconut oil will solidify and create clumps. If you notice this happening, you can set the mixing bowl on the warm part of your stovetop as the oven preheats or set the mixing bowl in a larger bowl of hot water until the coconut oil melts again. You just want to make sure you don’t get the batter too hot or the eggs will start cooking. Here’s a guide for how to bring things like butter, eggs and yogurt to room temp.
  • When combining your dry and wet ingredients make sure you mix until just combined and don’t over-mix, otherwise your muffins could turn out too dense or rubbery. It’s even okay if there are a few streaks of flour remaining as they’ll get mixed in when you add your mix-in of choice.
  • I highly recommend using silicone muffin liners or parchment baking cups for the best results and to prevent the muffins from sticking.
  • Let the muffins cool for a few minutes in the muffin tin and then remove to let cool completely on a wire rack. Don’t leave the muffins in the muffin tin for too long because they’ll continue to bake and could dry out!
  • If using paper liners, make sure to let the muffins cool completely before trying to remove the liners otherwise your muffins will likely stick.
Three blueberry yogurt muffins stacked on top of each other. The muffins are lined with paper wrappers.


What does adding yogurt to muffins do?

The yogurt helps to keep these muffins moist without a ton of oil and the acidity in yogurt helps activate the baking soda, which results in light and fluffy muffins.

What does yogurt replace in baking?

Yogurt is usually a healthier substitute for all or some of the fat in baked goods like butter or oil.

What type of yogurt is best to use?

I recommend using plain whole-milk Greek yogurt for this recipe. It’s what keeps these muffins moist and adds some protein. My go-to yogurt brands are Fage 5% plain Greek yogurt and Siggi’s plain whole milk yogurt. 2% Greek yogurt will also work, but I don’t recommend using non-fat Greek yogurt as it won’t add as much moisture to the muffins and it sometimes has fillers which could change the consistency.

Do I need to refrigerate muffins made with yogurt?

No. These yogurt muffins can be stored at room temperature, but they will last longer if stored in the fridge.

Can you freeze yogurt muffins?

Definitely! These muffins can be stored in the freezer for up to 3 months. Just make sure you’re storing them in a freezer-safe container or bag to prevent frostbite.


How to Store Leftovers

After allowing the muffins to cool completely, store in an airtight container for 3-4 days at room temperature or for up to 1 week in the refrigerator. For longer storage, you can freeze these muffins for up to 3 months in a freezer-safe container or bag. I like to use my Stasher bags for easy storage. To defrost, place muffins in the fridge overnight, at room temperature or defrost in the microwave.


More Muffin Recipes to Try

Be sure to check out all of my muffin recipes and the full collection of breakfast recipes here on EBF!

If you enjoyed this recipe, please consider leaving a ⭐ star rating and let me know how it went in the 📝 comments below.

5 from 7 votes

Yogurt Muffins

Here's how to make the best yogurt muffins with four different flavor variations. They're protein-packed, kid-friendly, easy to make and perfect for meal prep.
Prep Time: 10 minutes
Cook Time: 18 minutes
Total Time: 28 minutes
Servings: 12


Mix-Ins (choose one)

  • 1 cup chopped apples, plus more for topping
  • 1 cup chocolate chips, plus more for topping
  • 1 cup chopped strawberries, patted dry, plus more for topping
  • 1 cup blueberries, plus more for topping


  • Preheat oven to 400°F. Place 12 paper or silicone liners in your muffin tin.
  • In a large bowl, combine flour, baking powder, baking soda, salt and cinnamon.
  • In a medium mixing bowl, whisk together eggs, Greek yogurt, oil, maple syrup, almond milk and vanilla extract.
  • Pour the liquid mixture into the bowl with the dry ingredients and stir until mixture is just combined. Don’t over-mix! It’s okay if there are a few streaks of flour left.
  • Fold in mix-ins of choice, then evenly divide the batter into the prepared muffin tins. If you want to make a variety of flavors, divide the mixture evenly and add the appropriate amount of mix-ins. To make all four varieties, divide the mixture into quarters and add ¼ cup of each mix-in to each quarter of the batter.
  • Bake for 16-18 minutes or until a toothpick inserted in the center of the muffin comes out clean.
  • Let muffins cool in the tin for a few minutes, then remove so they don’t continue to cook and let cool completely on a wire rack.
  • Store at room temperature for 3-4 days or in the refrigerator for up to 1 week in an airtight container. You can also freeze for up to 3 months in a freezer-safe container.



Serving: 1muffin with no mix-ins | Calories: 161kcal | Carbohydrates: 22g | Protein: 4g | Fat: 7g | Saturated Fat: 5g | Monounsaturated Fat: 1g | Cholesterol: 34mg | Sodium: 181mg | Potassium: 43mg | Fiber: 2g | Sugar: 9g

Nutrition information is automatically calculated, so should only be used as an approximation.

Additional Info

Course: Breakast, Muffin
Cuisine: American
Keyword: yogurt muffins
Did you make this recipe?Mention @eatingbirdfood and tag #eatingbirdfood!

About Brittany

Hey there, I’m Brittany, the creator of Eating Bird Food, cookbook author, health coach and mama of two littles. Here you’ll find quick and easy recipes that make healthy fun and enjoyable for you and your family!

More about Brittany
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Recipe Rating


    1. Hi Rebecca – I bet honey or even monk fruit maple syrup would work fine as a substitute. Enjoy!

  1. Doesn’t baking kill all the probiotics in the yogurt? If that’s true, you should remove the claim that the muffins contain probiotics.

    1. Hi Tony – Thanks for reaching out. While it is true that baking yogurt will kill some of the probiotics, it will not kill all of them. The yogurt will still provide valuable nutrients! Hope you give these a try!

  2. 5 stars
    I made these today. I made 6 apricot and 6 strawberry. They turned out great. Simple and delicious.

    1. Ohh yummy! I’m so glad you enjoyed these muffins, Lyn. Thanks for making them and for coming back to leave a review. I so appreciate it!

    1. Yay! Glad to hear you are loving this recipe, Kate! Thank you so much for your review + star rating, I appreciate it!

  3. 5 stars
    I’ve made these a few times now and my husband and I love them! We prefer blueberries for an add in the most. Easy snack to throw in for lunch. Thank you for the recipe!

    1. Yay! I am so happy that you both enjoy this recipe, Lauren. Thank you so much for your review + star rating, I so appreciate you being here!

  4. 5 stars
    These are so good!I’ve eaten four already and don’t plan on stopping. Very simple, quick bake, lots of variations. I seperates into three and did strawberry, blueberry, and chocolate chips. Not too sweet, not bland, perfect for having with your morning cup of coffee, and tossing into a lunch box for your kid.

  5. I made these on Friday and they were so soft. I used fresh apricots and lily’s chocolate. I love your recipes! Thank you so very much!

      1. Hi Heather – I haven’t tested this recipe with GF flour, but I think it might work with 1:1 GF AP flour. Although I will mention, they might not be as fluffy, but should still be delicious! Let me know how they turn out if you give them a try, enjoy!