Healthy Chocolate Chip Muffins recipe made with whole wheat (or spelt) flour, no refined sugar and greek yogurt are healthy bakery style muffins with lots of mini chocolate chips. Make a double because these wholesome muffins will disappear in seconds!

Our other top two kid favorite muffins include almond flour banana muffins and healthy blueberry muffins. Although, no one ever seems to turn down any of these other healthy muffin recipes!

Healthy Chocolate Chip Muffins cooling on a baking rack

Healthy Chocolate Chip Muffins

All I can say about these healthy chocolate chip muffins is double-double the recipe. These easy mini chocolate chip muffins are light, fluffy, flavourful and loaded with mini chocolate chips.

Of course, your kids will gobble them up for healthy snacks and I love having one with my healthy iced coffee!

And that’s perfectly fine because these homemade muffins are made with 1/3 cup maple syrup, whole wheat flour and yogurt. Minus hydrogenated oils, refined sugar and chemicals found in store-bought mini breads. We are going to drop junk food sales one muffin at a time. Check out all of our healthy muffin recipes.

Kids also love these healthy homemade popsicles made with real fruit!

Why Make Chocolate Chip Muffin Recipe?

  • Wholesome ingredients: No hydrogenated oils, no refined sugars and a whole wheat chocolate chip muffin!
  • Light and fluffy: And so moist from the Greek yogurt. 
  • Easy to make: Made in one bowl and ready in less than 30 minutes, you can whip these up when the mood strikes.
  • Kid friendly: Contains decadent mini chocolate chips, need I say more? 
  • Versatile: Serve for breakfast, a lunchbox treat, in the afternoon or as a late night snack! 
  • Freezer friendly: Make a batch to eat now and freeze one for later. 

So, shall I show you how to use up those mini chocolate chips in your pantry? Like you needed help, I know. After these you can make some edible cookie dough, chocolate chip cookies, banana chocolate chip muffins, or healthy chocolate zucchini bread, too – yummy!

Healthy Chocolate Chip Muffin shown inside

Ingredients You Will Need

  • Yogurt: Regular 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 or learn how to make a 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. Just not granulated sugar because it will throw off the ratio of wet to dry ingredients in the muffin batter.
  • Flour: Whole wheat or spelt flour (like I use for these zucchini applesauce muffins) is the best and most nutritious. If you need gluten free, check out these almond flour muffins.

Although, I prefer to use 100% whole grains for muffins, if all purpose flour is what you have on hand, it can be used! Use 1 cup of all purpose white flour for every 3/4 cup of whole wheat flour that is called to use.

  • Oil: Any mild tasting oil like light olive oil, grapeseed or coconut oil (melt first). 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, like I use in healthy skillet cookie work, too. 🙂

I think my whole family is enjoying my healthy baking experiments- especially when there’s chocolate involved. I’ve already shared recipes for healthy chocolate bread, chocolate muffins, and healthy chocolate cake – and that’s not all!

mini chocolate chips egg whole grain flour maple syrup baking staples

How to Make Chocolate Chip Muffins

  • Preheat oven to 425 degrees F, spray non-stick 12 muffin tin with cooking spray or use muffin liners and set aside. These easy whole wheat chocolate chip muffins come together so fast, you oven will beep right when you are done filling muffin tin with batter.

I still spray my muffin tin even when using liners, just in case of batter overfill plus it makes it easier for removal and clean up.

  • Combine wet ingredients by whisking the egg first and then adding yogurt, oil, maple syrup, milk, vanilla, baking powder + soda.
  • Add flour and gently stir until well incorporated. Batter will be thick and that is ok!

Do not over mix the batter- otherwise 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 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 whole wheat chocolate chip muffins from the oven to wait for the temperature to come down.  This lower temperature will continue baking muffins inside.
  • Remove from the oven and let muffins cool for about 5 minutes.

Optional Add-In’s and Variations

  • Cinnamon: Just a pinch 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 muffin before baking.
  • Out of yogurt? Some readers have subbed mayo or sour cream- the recipe has not been tested like this, but it may work for you!
  • Orange zest: A small amount will give these muffins a nice zing!

Tips for Best Chocolate Chip Muffins

  • Spoon and level your flour: This is worth repeating anytime we are baking muffins! Spoon your flour into your measuring 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 batter into muffin tin.
  • 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 sliding out muffins like butter.


Can I make mini muffins?

Yes, bake for 10-12 minutes total – high heat for 3-4 minutes, and then reduce heat for remaining time until toothpick inserted comes out clean.

How do I make moist, not dry muffins?

You must use a yogurt with a fat content of 2% or higher for this recipe. That will result in moist muffins that are not dry!

How many calories does a chocolate chip muffin have?

A full sized muffin following this recipe exactly as written will have 225kcal. Depending on where you buy a chocolate chip muffin when it is made without these healthy swaps it can range anywhere from 400kcal up to 500kcal.

How do I adjust these for a convection oven?

Bake a few minutes less, always check using the toothpick method.

How do I know when muffins are done?

Using a toothpick, insert it into the center of the muffin. If the toothpick comes out clean (a few crumbs are okay), your muffins are ready to be removed from the oven.

Healthy Chocolate Chip Muffins on a cooling rack

Serving Recommendations

This will be the best chocolate chip muffin recipe you have ever tried. Make them and then ask your kids. Told ya 🙂

Making Muffins in Advance

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 making muffins in advance.

Storing: Store 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.

Freezing: Store in a freezer safe, resealable bag for up to 3 months. Muffins will defrost on the counter within 3-4 hours.

More Healthy Muffins Recipes

Chocolate Chip Muffins Recipe
Healthy chocolate chip muffins on a cooling rack.

Healthy Chocolate Chip Muffins

Healthy Chocolate Chip Muffins made with whole wheat (or spelt) flour, no refined sugar and greek yogurt are healthy bakery style muffins with lots of mini chocolate chips. Make a double batch because these wholesome muffins will disappear in seconds!
4.87 from 23 votes
Servings 12 muffins
Calories 225
Prep Time 7 minutes
Cook Time 18 minutes
Total Time 25 minutes



  • 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.
  • 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.


  • 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 egg.
  • Pumpkin: Substitute 1 cup yogurt with 1 cup pumpkin puree for pumpkin chocolate chip muffins (we love healthy pumpkin chocolate chip bread too).
  • Banana: Substitute 1 cup yogurt with 1 cup mashed banana for banana chocolate chip muffins.
See recipe post for more tips and FAQs.


Serving: 1muffin | Calories: 225kcal | Carbohydrates: 30g | Protein: 6g | Fat: 9g | Saturated Fat: 4g | Cholesterol: 15mg | Sodium: 170mg | Fiber: 3g | Sugar: 10g
Course: Dessert
Cuisine: North American
Author: Olena Osipov
Did you make this recipe?Mention @ifoodreal or tag #ifoodreal!

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About Olena

Welcome! I grew up in Ukraine watching my grandma cook with simple ingredients. I have spent the last 11 years making it my mission to help you cook quick and easy meals for your family!

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  1. 5 stars
    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 I’ve had success swapping 2% for 0% in the past), and it worked out perfectly! I can’t guarantee it will be that way for everyone, but I live on the coast so my environment is moist.

    Thank you for the recipe!

    1. I’m so happy to read this! Thanks for your positive feedback! Yes 0% could work if you live near the water, like you and me, it’s just for some muffins will lack flavor. But for some are OK.:)

    1. If you reduce it, you have to compensate with same amount of similar consistency ingredient. I would try regular yogurt or applesauce.

  2. 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 won’t be too dry!

  3. 5 stars
    I just made these and they’re AMAZING!! I did have to modify based on what I had. Here’s what I modified:

    1/2c 0% greek yogurt
    1/2c light sour cream
    Sugar free maple syrup
    All purpose flour (3c)
    Almond milk – 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.

  4. 5 stars
    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.

  5. 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

    1. Hi Janet. So this recipe uses more baking powder than others which has salt in it. If it’s possible to add leavening agents with wet ingredients and I know they will dissolve well, I do so. Some recipes it’s best to mix them with flour first and I know it’s 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.

  6. Can you post a link or image of the flour you use? Best I can find is whole wheat pastry flour, but I don’t quite understand the differences, and would like to try your recipes with the recommended flour to see the difference.

    1. Unfortunately, I don’t 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.

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