Chocolate Chip Yogurt Muffins
Published Jun 06, 2022, Updated Sep 27, 2023
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Protein packed chocolate chip yogurt muffins made with Greek yogurt, whole wheat flour and maple syrup. They’re light, fluffy and perfect for an on-the-go snack or breakfast.
Back with another flavor variation of my yogurt muffins! I’ve already shared a blueberry and strawberry version, but today I’m sharing a chocolate chip version because who doesn’t love chocolate chip muffins?
These muffins are very similar to my healthy chocolate chip muffins, but with even more protein-packed yogurt!
Why You Need to Make These Muffins
- They’re perfectly moist and fluffy and work for breakfast, snacking or even as dessert!
- They’re made with simple ingredients you likely already have in your kitchen.
- This is a great recipe to make with kids! They’ll love helping you mix all the ingredients together and will definitely love the chocolate chips in there. I know my little one is a big fan!
- whole wheat pastry flour – whole wheat pastry flour gives you the best of both worlds. You’ll get the light and fluffy texture that regular all-purpose flour provides, but still have the nutrients of whole wheat flour. My go-to brand is Bob’s Red Mill whole wheat pastry flour.
- unsweetened almond milk – I used unsweetened almond milk, but any type of milk will work, including cow’s milk. If you’re interested, here’s how to make homemade almond milk.
- eggs – helps bind the liquid and oil together. Make sure your eggs are at room temperature or they can make the coconut oil solidify while mixing.
- 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 make the muffins moist and fluffy! The oil also helps prevent the muffins from sticking to the liners.
- maple syrup – the natural sweetener of choice for these muffins. I haven’t tried making these with honey but it should just work as well.
- vanilla extract – a flavor enhancer.
- baking soda and baking powder – to help the muffins rise.
- salt – brings all of the flavors together.
- cinnamon – a nice warming spice for these muffins.
- chocolate chips – I like using Lily’s dark chocolate chips because they are low in calories and sugar, but any chocolate chips will work.
How to Make
Step 1: Start by combining the dry ingredients. In a large bowl, mix the flour, baking powder, baking soda, salt and cinnamon.
Step 2: In a medium bowl, whisk the eggs, yogurt, oil, maple syrup, almond milk and vanilla extract. Add the wet ingredients to the dry ingredients and stir until just combined. Fold in your chocolate chips.
Step 3: Line a muffin pan with paper or silicone muffin cups and then divide the batter evenly into the muffin tin. Top with extra chocolate chips.
Step 4: Bake at 400ºF for 18-20 minutes or until a toothpick inserted into the center of a muffin comes out clean. Let the muffins cool for a few minutes in the pan and then let cool completely on a wire rack.
pro tip! Make sure you don’t over-mix the batter or the muffins will be too dense after baking.
Tips for Success
- Make sure you’re using room temperature milk, eggs, maple syrup and Greek yogurt! If any of these ingredients are cool or cold, 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 blend 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 stir in the chocolate chips.
- 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. If you’re trying to speed up the process, place your muffins in the fridge to cool down quicker.
Yes! All-purpose flour will work just fine in place of whole wheat pastry flour.
I haven’t tested a gluten-free version of these muffins, but I would imagine using a 1:1 gluten-free all-purpose flour would work just fine in place of the whole wheat pastry flour. My favorite brand is Bob’s Red Mill gluten-free 1:1 all-purpose flour. I also have these almond flour muffins you could make if you’re looking for a chocolate chip muffin that’s gluten-free.
I haven’t tried it, but I would imagine using a non-dairy Greek-style yogurt or really any vegan yogurt would work just fine as a substitute for the Greek yogurt. Most chocolate chips contain dairy, so make sure to check the ingredients or go with my favorite, Lily’s dark chocolate chips. Enjoy Life chocolate chips are also vegan + dairy-free and would make for a great option!
I haven’t tested an egg-free version of these muffins, but let me know if you decide to experiment in the comments below! I would imagine using two flax eggs or chia eggs in place of the regular eggs would work just fine.
Totally! Feel free to make this recipe your own and customize the mix-ins. I bet even adding chopped nuts in with the chocolate chips would be delicious! You can also try my strawberry yogurt muffins and blueberry yogurt muffins!
I highly recommend using silicone muffin liners or parchment baking cups for the best results and to avoid the muffins from sticking too much. I also recommend spraying your liners with a little cooking spray. Also, make sure to let your muffins cool completely before trying to remove the liners otherwise they could stick. If you want, you can pop the muffins in the fridge to cool for an hour or so before removing the liners.
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 the muffins won’t rise as much.
How to Store Leftovers
After allowing the muffins to cool completely, store them 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
- Almond Flour Muffins
- Lemon Poppyseed Muffins
- Blueberry Yogurt Muffins
- Strawberry Yogurt Muffins
- Carrot Raisin Muffins
- Healthy Chocolate Muffins
- Healthy Chocolate Chip Muffins
- Oatmeal Banana Muffins
- Banana Blender Muffins
- Sweet Potato Muffins
Be sure to check out all of my muffin recipes here on EBF!
Chocolate Chip Yogurt Muffins
- 1 ¾ cups whole wheat pastry flour
- 1 teaspoon baking powder
- ¼ teaspoon baking soda
- ½ teaspoon sea salt
- ½ teaspoon cinnamon
- 2 large eggs, at room temperature
- 1 cup plain full fat Greek yogurt, at room temperature
- ¼ cup coconut oil, melted
- ½ cup maple syrup, at room temperature
- ¼ cup unsweetened almond milk, at room temperature
- 1 teaspoon vanilla extract
- 1 cup chocolate chips, 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 chocolate chips.
- Divide the batter evenly into the prepared muffin tins.
- Bake for 18-20 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.
- 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.
- Greek yogurt: I haven’t tried it, but I bet using a vegan yogurt would work just fine!
- Maple syrup: You can use agave, honey or even monk fruit maple syrup as a substitute for maple syrup.
- Almond milk: Any dairy-free or dairy milk will work in this recipe.
Nutrition information is automatically calculated, so should only be used as an approximation.