This Healthy Chocolate Chip Muffins recipe with whole wheat flour, Greek yogurt, lots of mini chocolate chips and no other refined sugar is perfect to make with the kids!
Other top kid favorite muffins include 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 the recipe. They are light, fluffy, flavorful and loaded with mini chocolate chips.
These healthy muffins are perfect for a healthy snack or even breakfast!
Why Youโll Love This Recipe
- Kids love them: Kids love anything โmuffinsโ and chocolate chips help a lot!
- Better ingredients: Made with only 1/3 cup maple syrup, whole wheat flour and yogurt. Minus hydrogenated oils and refined sugar found in store-bought muffins.
- Simple ingredients: Made with everyday staples so you can whip up these healthy chocolate chip muffins when the mood strikes.
- Easy recipe: Made in one bowl and ready in less than 30 minutes.
Readerโs Review
We love these muffins. Made them for breakfast and my kids loved them. They are so soft, fluffy, and delicious. Thank you Olena!!!
Kayla
Ingredients for Healthy Chocolate Chip Muffins
- 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: Use liquid sweetener like honey, brown rice syrup, agave etc. is OK to use.
- 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: The best choice is mild tasting oil like avocado oil, light olive oil, grapeseed oil or melted coconut oil.
- Chocolate chips: I prefer mini chocolate chips because you get more in every bite and they look super cute. But semi sweet or dark chocolate chips work too.
How to Make Healthy Chocolate Chip Muffins
- Whisk wet ingredients: In a large bowl, whisk the egg. Then add the yogurt, oil, maple syrup, milk, vanilla, baking powder and baking soda.
- Finish the batter: Add whole wheat flour and gently stir until well incorporated. Muffin batter will be thick and that is OK. Add chocolate chips and give a few more gentle stirs. Then divide batter between 12 openings of a regular size muffin tin.
- Bake at 425 F for 7 minutes: A higher baking temperature in the beginning will take care of high muffin tops.
- Reduce heat to 375 F and bake for another 10-11 minutes: Or until a toothpick inserted in the centre comes out clean. No need to remove muffins from the oven to wait for the temperature to come down. Then remove muffins 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 wonโt be as moist. I recommend to use at least 2%, thatโs what I used.
- Do not over mix the batter: Otherwise muffins will be tough and rubbery.
- This silicone muffin tin makes muffins slide out like butter.
- No chocolate chips? If you have a chocolate bar, chop it into chunks.
Variations
- 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.
- Orange zest: A small amount of orange zest will give these muffins a nice zing.
- Pumpkin: Substitute 1 cup of yogurt with 1 cup of pumpkin puree for pumpkin chocolate chip muffins. A version of my healthy pumpkin chocolate chip bread.
How to Store
Store: Store muffins in a cool dry place for up to 3-4 days. I like to place them 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 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.
FAQs
Some readers have subbed sour cream instead. I also think replacing yogurt with pumpkin puree or mashed banana on 1:1 ratio should be fine.
Yes. Use 1 cup of all-purpose white flour for every 3/4 cup of whole wheat flour this 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 in mind that 1 cup of oat flour weighs 90 grams and 1 cup of wheat flour weighs 120 grams.
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.
More Healthy Muffin Recipes to Try
- Zucchini chocolate chip muffins
- Chocolate zucchini muffins
- Pumpkin banana muffins
- Healthy banana muffins
- Almond flour banana muffins
Healthy Chocolate Chip Muffins
Equipment
Ingredients
- 1 large egg
- 1 cup plain 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 tablespoon pure vanilla extract
- 1 tablespoon baking powder
- 1/4 teaspoon 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, baking 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: Freeze in an airtight container for up to 3 months. Thaw on the counter for 2-3 hours.
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
These look great and I want to make them, however, I have a question I hope you can help answer!
I want to add a little bit of vanilla protein powder, just to give it a little protein boost. Iโm not looking to add a bunch, maybe only a few tablespoons evenโฆbut donโt want to mess with the texture and I donโt know how to adjust accordingly. Any suggestions?
Hi Ali. Yes, you can add a few tablespoons or even 1/4 cup only of whey protein powder. Plant-based protein powder is very absorbing, so that wouldnโt work. You can also add a few scoops of collagen. Hope this helps.
I love this recipe. Itโs easy and very fast to bake it..if it is possible the temperature of oven also in Celsius (..) .
Fantastic! Glad you enjoyed the recipe!
I didnโt have yogurt so I blended cottage cheese, Iโm hoping this ups the protein for my kiddos. I missed the note about adding the baking powder with the wet ingredients. 1 tablespoon seems excessive and these muffins had a bit of a salty taste. Iโll try them again and add the baking powder with the wet ingredients next time. Hopefully that helps.
Hi Elizabeth. Your muffins had a salty taste because you used cottage cheese, it is quite higher in sodium than yogurt. Hope your next try turns out well!
I just made these this afternoon, and they were a hit! My mom really enjoyed them.
I know you said not to use 0% fat yogurt, but I wanted to try it anyway (because Iโve had success swapping 2% for 0% in the past), and it worked out perfectly! I canโt guarantee it will be that way for everyone, but I live on the coast so my environment is moist.
Thank you for the recipe!
Iโm so happy to read this! Thanks for your positive feedback! Yes 0% could work if you live near the water, like you and me, itโs just for some muffins will lack flavor. But for some are OK.:)
Can I use less maple syrup?
If you reduce it, you have to compensate with same amount of similar consistency ingredient. I would try regular yogurt or applesauce.
These are in the oven now but wanted to add that the note about 0% yogurt would have been useful in the actual recipe, instead of a note. Fingers crossed they wonโt be too dry!
Next to Greek yogurt ingredient it says โ2%+โ yogurt, in the actual recipe. Fingers crossed!
I just made these and theyโre AMAZING!! I did have to modify based on what I had. Hereโs what I modified:
1/2c 0% greek yogurt
1/2c light sour cream
Sugar free maple syrup
All purpose flour (3c)
Almond milk โ unsweetened vanilla
They were super moist. Given the lack of butter/sugar I was surprised the kids loved them! I made big muffins so cooked at the lower temp for abut 10 or 11 minutes.
Glad everyone enjoyed it!
My 4 year old son staple in his diet at the moment is this muffin recipe. Instead of chocolate chips I use every type of fruit cut up. I use apples, pears, peaches, blueberries, raspberries etc. He loves them! Knowing the muffin is on his tray, he eats the other food as well. Thank you so much for such a great recipe.
I love that and that it helps him eat his other food too!
I have made several muffin recipes on your website and they all had salt. Tonight I made Healthy Chocolate Chip Muffins and there is no salt listed. Also in this recipe the baking powder and baking soda are added with the wet ingredients rather than the dry ones. Could you please explain the reason? Thanks
Hi Janet. So this recipe uses more baking powder than others which has salt in it. If itโs possible to add leavening agents with wet ingredients and I know they will dissolve well, I do so. Some recipes itโs best to mix them with flour first and I know itโs a golden rule in baking BUT more often I mix them with wet and muffins work. As long as they are not lumpy and are distributed evenly.
Can you post a link or image of the flour you use? Best I can find is whole wheat pastry flour, but I donโt quite understand the differences, and would like to try your recipes with the recommended flour to see the difference.
Unfortunately, I donโt have a picture of the whole wheat flour used in the recipe, but most often spelt flour is used interchangeable (and you can find a photo of the brand used in the ingredients picture of healthy cranberry muffins). The main difference between whole wheat pastry flour and whole wheat flour is that the pastry version is milled from low protein soft spring wheat whereas whole wheat flour is milled from winter wheat. You should be able to find whole wheat flour in the grocery baking section near other flours, most major brands carry whole wheat flour. That being said, you may be able to substitute whole wheat pastry flour for whole wheat flour with the same results.