by Olena

Healthy Chocolate Chip Muffins

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Olena Osipov
4.8 from 16 votes

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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 batch because these wholesome muffins will disappear in seconds!

Our other top two kid favorite muffins for easy breakfasts or snacks include almond flour banana muffins and healthy blueberry muffins. Although, no one ever seems to turn down any of these other favorite 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 and I love having one with my 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.

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, choc chip pumpkin bread, 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 or 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 muffins) is the best and most nutritious. If you need gluten-free, check out this muffin recipe with almond flour.

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 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 quinoa muffins, 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.
  • Egg-Free: Use a flax egg or chia egg.
  • Pumpkin: Substitute 1 cup yogurt with 1 cup pumpkin puree for pumpkin chocolate chip muffins (we love this bread too).
  • 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.

FAQs

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

Healthy Chocolate Chip Muffins {Moist and Fluffy!}

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!
4.82 from 16 votes
Print Save Rate
Course: Dessert
Cuisine: North American
Prep Time: 7 minutes
Cook Time: 18 minutes
Total Time: 25 minutes
Servings: 12 muffins
Calories: 225kcal
Author: Olena Osipov

Ingredients

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.
    Healthy Chocolate Chip Muffins
  • Add flour and gently stir until well incorporated (batter will be thick). Do not over mix otherwise muffins will be tough.
    Healthy Chocolate Chip Muffins
  • Add chocolate chips.
    Healthy Chocolate Chip Muffins
  • Give a few more gentle stirs. Then, using an ice cream scoop, divide batter between 12 openings.
    Healthy Chocolate Chip Muffins
  • 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.
    Healthy Chocolate Chip Muffins
  • Remove from the oven, let muffins cool for about 5 minutes and transfer to a cooling rack to cool off completely.
    Healthy Chocolate Chip Muffins

Store: Store in a cool dry place for up to 3-4 days or freeze for up to 3 months.

    Notes

    • 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. Spend your time finding whole milk plain yogurt 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.
    • Egg Free: Make 1 flax egg or chia egg to replace egg.
    • Pumpkin: Substitute 1 cup yogurt with 1 cup pumpkin puree for pumpkin chocolate chip muffins (we love this bread too).
    • Banana: Substitute 1 cup yogurt with 1 cup mashed banana for banana chocolate chip muffins.
    • Pinch of cinnamon or nutmeg: Will add a subtle warmth to the muffin.
    See recipe post for more tips and FAQs.

    Nutrition

    Serving: 1muffin | Calories: 225kcal | Carbohydrates: 30g | Protein: 6g | Fat: 9g | Saturated Fat: 4g | Cholesterol: 15mg | Sodium: 170mg | Potassium: 205mg | Fiber: 3g | Sugar: 10g | Vitamin A: 20IU | Calcium: 143mg | Iron: 1mg
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    37 comments on “Healthy Chocolate Chip Muffins

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    1. 5 stars
      Hi, I do not function well in a kitchen. Making these intimidated me. However, I was delighted and pleasantly surprised by the end result 🙂 But, OOPS, I thought I bought plain greek yogurt, but it was coconut.

    2. 5 stars
      Hello !
      I tried this recipe and it was delicious !
      My co-workers loved it too 🙂
      I realized that I am using a convection oven, because it was a bit overcooked, I think you are using a conventional oven, isn’t it?
      It was still very good, thank you for your recipes that are always wonderful !

      Mélanie ~ France

      1. I am so happy to hear everyone enjoyed my muffins. I use regular oven when baking recipes, that’s default because many people don’t have convection. Just cook a bit less next time. 🙂

    3. Have you used or do you think oat flour could be substituted for some of the flour? I made your almond flour banana muffins today and they were amazing, would love to try these for my kiddos.

      1. Hi Jess. Oat flour and whole wheat flour are not interchangeable. You can use all purpose flour or spelt flour.

    4. 4 stars
      These turned out really good. I used whole milk greek yogurt, pure maple syrup, light olive oil, and 1/4c unsweetened apple sauce for the egg. Thanks Olena for the recipe and the healthly substitutions.

    5. 5 stars
      We love these muffins. Made them for breakfast and my kids loved them. They are so soft, fluffy, and delicious. Thank you Olena!!

    6. I use Almond flour in my cooking. What ratio should I use when recipe says whole wheat flour please. Glenys

    7. 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

    8. 4 stars
      The muffins are good but I only needed about nine mins to cook and it was perfect. Definitely recommend.

    9. 5 stars
      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!

    10. 5 stars
      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 🙂

    11. 5 stars
      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!

      1. 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!

    12. 5 stars
      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!

    13. 5 stars
      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!

    14. 5 stars
      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!

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