Healthy Chocolate Chip Muffins recipe made with whole wheat flour, no refined sugar and Greek yogurt are healthy bakery style muffins with lots of mini chocolate chips.
Our other top kid favorite muffins include healthy banana chocolate chip muffins, pumpkin chocolate chip muffins and healthy chocolate muffins.
Table of Contents
All I can say about these healthy chocolate chip muffins is to double-double the recipe. These healthy muffins are light, fluffy, flavourful and loaded with mini chocolate chips.
Of course, your kids will gobble them up for a healthy snack. And that’s perfectly fine because this healthy chocolate chip muffin recipe is made with only 1/3 cup maple syrup, whole wheat flour and yogurt. Minus hydrogenated oils, refined sugar and chemicals found in store-bought muffins.
We are going to drop junk food sales one healthy chocolate chip muffin at a time!
Ingredients You Will Need
To make healthy chocolate chip muffins you will need just a few simple ingredients. No hydrogenated oils and no refined sugars in this healthy muffin recipe!
- Yogurt: Regular yogurt or Greek yogurt with fat content of 2% and higher. Non-fat yogurt will make muffins less moist.
- Egg: You can sub egg with chia seed egg, flax egg or 1/4 cup applesauce or mashed banana.
- Milk: Any milk works. I used dairy-free unsweetened almond milk.
- Maple syrup: Any liquid sweetener like honey, brown rice syrup, agave etc. is OK to use to make these healthy chocolate chips muffins.
- Flour: Any whole grain flour like whole wheat flour, spelt flour, white whole wheat flour or whole wheat pastry flour. Please see FAQs for other flours.
- Oil: Any mild tasting oil like light olive oil, grapeseed oil or melted coconut oil. I tend to stay away from vegetable oil, but if it is all you have on hand, it would work.
- Chocolate chips: I prefer mini chocolate chip muffins because you get more in every bite and they look super cute. But regular or dark chocolate chips work too.
How to Make Healthy Chocolate Chip Muffins
Made in one bowl and ready in less than 30 minutes, you can whip up these healthy chocolate chip muffins when the mood strikes.
In a large bowl, combine wet ingredients by whisking the egg first and then adding yogurt, oil, maple syrup, milk, vanilla, baking powder and baking soda.
Add whole wheat flour and gently stir until well incorporated. Muffin batter will be thick and that is OK. Do not over mix it, otherwise healthy chocolate chip muffins will be tough.
Add chocolate chips and give a few more gentle stirs. Then divide batter between 12 openings of a regular size muffin tin.
Bake muffins in 425 degrees F preheated oven for 7 minutes. A higher baking temperature in the beginning will take care of high muffin tops.
Reduce heat to 375 degrees F and bake for another 10-11 minutes or until a toothpick inserted in the centre comes out clean. No need to remove chocolate chip muffins from the oven to wait for the temperature to come down. This lower temperature will continue baking muffins inside.
Remove muffins from the oven and let them cool on a wire rack for about 5 minutes.
Tips for Best Results
Here are my top tips and tricks for the best healthy chocolate chip muffins in the world!
- Spoon and level your flour: This is worth repeating anytime we are baking muffins. Spoon your flour into your measuring cup, rather than scooping, then level off with a knife.
- Please avoid 0% yogurt, muffins won’t be as moist. Invest time in locating whole milk yogurt in your area and buy it from now on. So much healthier than non-fat.
- No chocolate chips? If you have a chocolate bar, chop it into chunks.
- Use an ice cream scoop for placing muffin batter into the muffin pan.
- Pumpkin: Substitute 1 cup yogurt with 1 cup pumpkin puree for pumpkin chocolate chip muffins. A version of my healthy pumpkin chocolate chip bread.
- Banana: Substitute 1 cup yogurt with 1 cup mashed banana for banana chocolate chip muffins.
- This silicone muffin tin makes muffins slide out like butter.
Variations
Here are a few ideas to make your healthy chocolate chip muffins more fun!
- Cinnamon: Just a pinch of cinnamon can add a subtle warmth.
- Nutmeg: Not a fan of cinnamon, use a pinch of nutmeg for a nutty warm taste.
- Sea salt: A pinch of sea salt included in the batter can help bring out the flavor.
- Sugar topping: Sprinkle a small amount of cane sugar on the top of each chocolate chip muffin before baking.
- Out of yogurt? Some readers have subbed sour cream instead.
- Orange zest: A small amount of orange zest will give these muffins a nice zing.
FAQs
Yes. Use 1 cup of all-purpose white flour for every 3/4 cup of whole wheat flour that this healthy chocolate chip muffins recipe calls for.
You may be able to use 1:1 ratio of all-purpose gluten free flour to replace whole wheat flour. I would also add a splash of milk then. Coconut flour or almond flour will not work. You can also use oat flour by weight, keeping mind that 1 cup of oat flour weighs 90 grams and 1 cup of wheat flour weighs 120 grams.
No. You have to use a liquid sweetener. Granulated sugar will throw off the ratio of wet ingredients to dry ingredients in the muffin batter.
You must use a yogurt with a fat content of 2% or higher for this muffin recipe. That will result in moist muffins that are not dry!
Yes, bake mini chocolate chip muffins for 10-12 minutes total. First on high heat for 3-4 minutes, and then reduce heat for remaining time until toothpick inserted comes out clean.
What to Serve Healthy Chocolate Chip Muffins With?
Besides the traditional glass of cold milk, here are a few serving ideas for your healthy chocolate chip muffins recipe!
- Toppings: A dollop of Greek yogurt, nut butter, or honey butter is delicious.
- Fruit: Berries, orange slices, a banana or even small bowl of applesauce.
- Brunch: Along with healthy breakfast casserole or on a brunch charcuterie board.
- Dessert: A scoop of healthy dairy free vegan vanilla ice cream or chocolate ice cream.
How to Store
I am laughing as I write this. I am afraid you will not have many muffins to store past day one! But just in case you at least doubled the recipe, here are the easy methods for storing the muffins.
Store: Store healthy chocolate chip muffins in a cool dry place for up to 3-4 days. I like to place muffins in a resealable plastic bag and keep a bit of an opening to prevent condensation build up and complete moisture loss.
Another option to absorb excess moisture build up when storing them, is to line the bottom of your container with a paper towel then place another paper towel on top of the muffins.
Freeze: Store in an airtight container or a freezer safe, resealable bag for up to 3 months. Muffins will defrost on the counter within 3-4 hours.
Storage Tip
Check out my detailed posts how to store muffins and how to freeze muffins for all my best tips and tricks.
More Healthy Muffin Recipes to Try
- Chocolate zucchini muffins
- Zucchini chocolate chip muffins
- Chocolate coconut flour muffins
- Protein muffins
- Healthy banana muffins
- Almond flour banana muffins
- Pumpkin chocolate chip bread
Healthy Chocolate Chip Muffins
Equipment
Ingredients
- 1 large egg
- 1 cup plain regular yogurt or Greek yogurt 2%+ fat
- 1/4 cup avocado oil or any mild tasting oil
- 1/3 cup maple syrup or honey
- 1/2 cup any milk I used unsweetened almond milk
- 1 tbsp pure vanilla extract
- 1 tbsp baking powder
- 1/4 tsp baking soda
- 2 1/3 cups whole wheat or spelt flour
- 3/4 cup mini chocolate chips
- Cooking spray I use Misto
Instructions
- Preheat oven to 425 degrees F and spray muffin tin with cooking spray. Set aside. In a large mixing bowl, whisk the egg for 10 seconds. Add yogurt, oil, maple syrup, milk, vanilla, baking powder + soda, and whisk to combine.
- Add flour and gently stir until well incorporated (batter will be thick). Do not over mix otherwise muffins will be tough.
- Add chocolate chips and give a few more gentle stirs. Then, using an ice cream scoop, divide batter between 12 openings.
- Bake for 7 minutes in preheated to 425 degrees F oven. Reduce heat to 375 degrees F (no need to wait for oven to cool off) and bake for another 10-11 minutes or until a toothpick inserted in the centre comes out clean.
- Remove from the oven, let muffins cool for about 5 minutes and transfer to a cooling rack to cool off completely.
Notes
- Store: Store in a cool dry place for up to 3-4 days.
- Freeze: Up to 3 months.
- For all purpose flour, use 1 cup of white flour for every 3/4 cup of whole wheat flour that recipe calls for.
- Please avoid 0% yogurt, muffins won’t be as moist.
- No chocolate chips? If you have a chocolate bar, chop it into chunks.
- Egg Free: Make 1 flax egg or chia seed egg to replace the egg.
If i want ti use white flour instead, How much white flour do i use in this recipe? The measurement is given but i didnt quite understand it.
Thank you
It will be 3 cups of white flour.
The best spelt muffin I have come across the internet!!! Moist and so soft!!! Super Yummmm!!!
Thanks for sharing your positive feedback Arlene!
The muffins are good but I only needed about nine mins to cook and it was perfect. Definitely recommend.
This recipe is magic. I never seem to have every ingredient in hand at one time, but no matter which substitutuin I make, they are always amazing! I’ve subbed mayo or sour cream for the Greek yogurt (not as healthy, I know), flax egg for the egg, coconut oil for the olive oil, maple syrup or even a bit of molasses for the honey. Always use dark chocolate chips ..and they are always perfect. My pickiest eater would eat then every day if I kept them stocked! Thank you!
Hi Michelle! It made my day that you called my healthy muffins MAGIC! Thanks!
Best. Muffins. Ever! Everyone loves them. Super moist. Super easy to make. So glad I came across your website. Thanks from a fellow Vancouver island chick 🙂
Oh yay. Where do you live?
I made these as mini muffins. I followed the recipe exactly and then baked them for 10 minutes. I can’t believe something I baked actually came out so delicious. They are incredibly moist and chewy. Thanks for the recipe!
Why not?!:) If you follow recipes for a while, you get a hang of cooking and can be a very good cook yourself. Enjoy and you are welcome!
These turned out great! I substituted apple sauce for the olive oil and they turned out perfect. I wasn’t sure about the tablespoon of baking powder because I’ve never used that much in a recipe, but it worked! 🙂 They were light, fluffy and delicious. I also used Whole Milk Greek Yogurt because my little one needs all the protein and fats she can get!
Awesome! Glad you enjoyed and followed the recipe!:)
I just made these for my very picky toddler and he loves it! He keeps saying “yum! Thank you mommy!” I subbed a chia seed egg for the regular egg. I’d like to make them again and play with the proportions to incorporate some rolled or quick oats. Thanks for the recipe!
These were delicious and moist. I used white flour because my kids would know it’s whole wheat right away. Followed teh recipe and didn’t over stir. Muffins were amazing!
The last two times I tried making muffins I failed miserably, but looking at these now… It’s time to try again.
IF you follow the recipe and use exact ingredients, you will be fine this time.:)