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.

Healthy chocolate chip muffins on a wire rack.

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!

Almond milk, Greek yogurt, egg, baking powder, baking soda, vanilla, chocolate chips, maple syrup, oil, whole wheat flour.
  • 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.

Liquid ingredients and baking staples in blue bowl.

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.

Whole wheat flour with wet ingredients in blue bowl with spatula.

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.

Healthy chocolate chip muffins batter in blue bowl.

Add chocolate chips and give a few more gentle stirs. Then divide batter between 12 openings of a regular size muffin tin.

Healthy chocolate chip muffins in red silicone muffin tin ready to bake.

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.

Healthy chocolate chip muffins on a cooling rack.

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.
Closeup of healthy chocolate chip muffin showing texture inside.


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.


Can I use all-purpose flour in this healthy chocolate chip muffin recipe?

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.

Can I use any gluten-free flour?

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.

Can I use granulated sugar?

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.

How do I make healthy chocolate chip muffins moist?

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!

Can I make mini muffins?

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!

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

Healthy chocolate chip muffins in red silicone muffin tin on top of wire rack.
Healthy chocolate chip muffins on a cooling rack.

Healthy Chocolate Chip Muffins

Healthy Chocolate Chip Muffins with whole wheat flour, no refined sugar and greek yogurt. Delicious bakery style healthy muffins!
4.87 from 29 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 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.


  • 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.


Serving: 1muffin | Calories: 225kcal | Carbohydrates: 30g | Protein: 6g | Fat: 9g | Saturated Fat: 4g | Cholesterol: 15mg | Sodium: 170mg | Fiber: 3g | Sugar: 10g
Course: Muffins and Quick Bread
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. 4 stars
    I didn’t have yogurt so I blended cottage cheese, I’m 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. I’ll try them again and add the baking powder with the wet ingredients next time. Hopefully that helps.

    1. 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!

  2. 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.

  3. 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!

  4. 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.

  5. 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.

  6. 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.

  7. 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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