Healthy Chocolate Chip Muffins
Published Feb 18, 2022, Updated Mar 29, 2023
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These healthy chocolate chip muffins are soft, fluffy, perfectly moist and absolutely delicious. They’re made with whole wheat flour, Greek yogurt, maple syrup and studded with chocolate chips.
I’ve been on a muffin kick lately! Recently I’ve shared blueberry yogurt muffins, healthy chocolate muffins and now these healthy chocolate chip muffins.
In true EBF fashion, I decided to put a healthier spin on these muffins by using whole wheat flour instead of white flour, coconut oil instead of butter, Greek yogurt to replace some of the oil and maple syrup instead of white sugar. They taste delicious and are guaranteed to become a new family favorite!
Why You’ll Love These Muffins
- They’re made with simple ingredients that you likely already have on hand.
- They’re healthy and delicious and will hit the spot for breakfast, a snack or even dessert!
- This is a great recipe to make with kids! They’ll love helping you pour ingredients into the bowl and mix and will obviously love the end result.
- whole wheat pastry flour – whole wheat pastry flour works better than regular whole wheat flour if you’re looking for the light and fluffy texture that regular all-purpose flour provides, but still want the nutrients of whole wheat flour. My go-to brand is Bob’s Red Mill whole wheat pastry flour.
- baking soda and baking powder – to help the muffins rise.
- unsweetened almond milk – make your own vegan “buttermilk” by mixing apple cider vinegar with almond milk (store-bought or homemade almond milk works)! Whisk the ACV and almond milk and set aside at room temperature. The mixture should bubble, thicken and potentially even curdle after a few minutes. Not all non-dairy milk will work for vegan buttermilk but soy milk does if you don’t have almond milk on hand.
- apple cider vinegar – when shopping for ACV, look for a brand that’s unpasteurized with “the mother” included. This is where all the nutrients are. I personally recommend Bragg’s apple cider vinegar. It’s organic, raw and the best of the best.
- salt – brings all of the flavors together.
- 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.
- cinnamon – a nice warming spice for these muffins.
- vanilla extract – a flavor enhancer.
- maple syrup – the natural sweetener of choice for these muffins. I haven’t tried making these with honey but that should work as well.
- coconut oil – helps make the muffins moist and fluffy! The oil also helps prevent the muffins from sticking to the liners.
- chocolate chips – I like using Lily’s dark chocolate chips because they are low in calories and sugar.
How to Make Healthy Chocolate Chip Muffins
Step 1: Whisk almond milk and apple cider vinegar in a medium mixing bowl and let curdle for 5-10 minutes. Set aside.
Step 2: In a large mixing bowl combine flour, baking powder, baking soda, cinnamon and salt.
Step 3: In the same mixing bowl as milk, add eggs, maple syrup, Greek yogurt, melted coconut oil and vanilla extract. Whisk until combined.
Step 4: Pour the wet ingredients into the bowl with the dry ingredients and stir until just combined. Make sure you don’t over-mix or the muffins will be too dense after baking. Fold in your chocolate chips.
Step 5: Line a muffin tin with paper or silicone muffin liners and then divide batter evenly into muffin tin. Top with extra chocolate chips.
Step 5: Bake at 350ºF for 20-22 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.
- 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 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 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.
Frequently Asked Questions
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 haven’t tested a vegan version of these muffins, but you can easily swap the Greek yogurt for a vegan yogurt and I bet using flax eggs or chia eggs would work! If you decide to experiment, let me know in the comments below!
Swap the Greek yogurt with any yogurt of choice! I would just avoid flavored yogurts or anything with lots of added sugars.
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.
How to Store Healthy Chocolate Chip Muffins
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
- Chocolate Chip Yogurt Muffins
- Healthy Pumpkin Muffins
- Almond Flour Muffins
- Lemon Poppyseed Muffins
- Strawberry Protein Muffins
- Flourless Zucchini Muffins
- Oat Bran Muffins
- Flourless Pumpkin Muffins
- Oatmeal Banana Muffins
- Apple Yogurt Muffins
- Protein Muffins
- Banana Blender Muffins
Be sure to check out all of my muffin recipes and the full collection of breakfast recipes here on EBF!
Healthy Chocolate Chip Muffins
- ¾ cup unsweetened almond milk, at room temperature
- 3 teaspoons apple cider vinegar
- 1 ¾ cup whole wheat pastry flour
- 1 teaspoon baking powder
- ½ teaspoon baking soda
- ½ teaspoon cinnamon
- ½ teaspoon sea salt
- 2 large eggs, at room temperature
- ½ cup pure maple syrup, at room temperature
- ½ cup plain whole milk Greek yogurt, at room temperature
- ¼ cup coconut oil, melted
- 1 teaspoon vanilla extract
- 1 cup chocolate chips, plus more for topping
- Preheat oven to 350°F. Line a 12 cup muffin pan with paper or silicone liners.
- Whisk almond milk and apple cider vinegar in a medium bowl and let curdle for 5-10 minutes. Set aside.
- In a large bowl combine flour, baking powder, baking soda, cinnamon and salt.
- In the same bowl as milk, add eggs, maple syrup, Greek yogurt, coconut oil and vanilla extract. Whisk until combined.
- Pour the wet ingredients into the bowl with the dry ingredients and stir until just combined. Don’t overmix!
- Fold in chocolate chips and evenly divide the batter evenly between the 12 muffin cups. Top with extra chocolate chips.
- Bake for 20-22 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.
- 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: Any yogurt will work here!
- Maple syrup: You can use agave, honey or even monk fruit maple syrup as a substitute for maple syrup.
Nutrition information is automatically calculated, so should only be used as an approximation.
Brittany, if I wanted to make chocolate chocolate chip muffins, how much cocoa should I use and should I either alter the liquid or flour to compensate?
Thank you Brittany, I love your recipes!
Hi Dianna, I have a healthy chocolate muffin recipe you could try instead – it has chocolate chips too!
Could I substitute coconut oil with Avocado oil? I can’t digest coconut oil well.
Hi, Abby! That should be a fine substitution, though I haven’t tried it. Let me know how it turns out for you!
These muffins taste just like a chocolate chip cookie. They are healthy and delicious. The best part is, my family thought they were eating a real treat and everyone wanted seconds.
Hi, Kara! I’m so glad this recipe was a hit with your family. Thanks for making these muffins and coming back to leave a review, I really appreciate it!
excellent post thank you for sharing
Made these yesterday for my girls and I and they are delicious! I made them vegan with flax eggs and vegan green yogurt, and used soy milk instead of almond Bc that’s what I had. Also used half wheat and half AP flour! They turned out so yummy!
Woo! Thanks for sharing your substitutions, Caitie! I’m so glad these muffins turned out for you and your family. 🙂
Made these today for my son and they were delicious! Texture is perfectly fluffy and they have so much flavor. I used 1/3 cup maple syrup and coconut yogurt and it was perfect. Thanks for another great one 🙂
Woo! So glad this recipe turned out for you, Cristina! Thanks for leaving a review, I really appreciate it.
These muffins were really yummy! How do I keep the chocolate chips from sinking to the bottom? Even the chips I put on top of each muffin sank. Was my batter too thin?
Hmmm, it’s possible your batter was too thin. Did you change anything about the recipe?
I used Bob’s 1:1 Gluten Free AP flour. But of course its possible that I measured something incorrectly.
I would think the 1:1 would have the same results as the whole wheat pastry flour, but if that’s the only thing different, perhaps that is the issue. My other thoughts are different, larger chocolate chips could be the issue? You could try adding 1 Tablespoon of batter in the bottom of the liners without the chocolate chips and then mixing in the chocolate chips to the rest of the batter and distributing, that could help!
I used min chips. I’m just going to assume I measured a liquid ingredient to liberally. Still yummy though and I will make them again.
That’s always possible! I’m glad to hear you’ll give them another shot. Thanks, Lauren!
Can I use all regular whole wheat flour, or just it be mixed with all purpose?
Hi Cloey – Yes, you can use regular whole wheat flour, but I will say that whole wheat pastry flour works better than regular whole wheat flour if you’re looking for the light and fluffy texture that regular all-purpose flour provides, but still want the nutrients of whole wheat flour. If you give it a try with regular whole wheat four, let me know how you like it!