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!
Table of contents
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, choc chip pumpkin bread, banana chocolate chip muffins, or healthy chocolate zucchini bread, too – yummy!
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 quinoa muffins, chocolate muffins, and healthy chocolate cake – and that’s not all!
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 (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
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.
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!
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.
Bake a few minutes less, always check using the toothpick method.
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.
Serving Recommendations
- 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.
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
- Healthy carrot muffins
- Healthy banana muffins
- Healthy pumpkin muffins
- Healthy chocolate muffins
- Almond flour blueberry muffins
You might also enjoy this recipe for chocolate protein cookies or healthy zucchini brownies!
Healthy Chocolate Chip Muffins
Ingredients
- 1 egg large
- 1 cup regular or Greek yogurt plain (2%+ fat)
- 1/4 cup avocado oil or any mild tasting
- 1/3 cup maple syrup or honey
- 1/2 cup any milk I used unsweetened almond
- 1 tbsp pure vanilla extract
- 1 tbsp baking powder aluminum free
- 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.
- 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 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.
- 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 this bread too).
- Banana: Substitute 1 cup yogurt with 1 cup mashed banana for banana chocolate chip muffins.
Nutrition
Recipes and images are a copyright of ifoodreal.com. It is against the law to republish recipes without permission. Nutritional info is approximate.
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.
So glad to hear of the kitchen success! I am sure the coconut yogurt added a nice nutty taste! 🙂
1. Can cassava, cauliflower or any other flour be used ?
2. Can lactose free yogurt be used?
Thank you
1 is no and 2 is yes.
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
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. 🙂
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.
Hi Jess. Oat flour and whole wheat flour are not interchangeable. You can use all purpose flour or spelt flour.
By far the best dessert I have ever made and so simple and quick!
Thank you for taking the time to write such a positive review Chrissy!
Thank you for this! We loved the maple syrup and Greek yogurt! So easy to make!
You are very welcome Bill 🙂
They came out perfect! Just the right texture, flavor, and appearance.
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.
You are very welcome Crystal!
I LOVE MUFFINS
We love these muffins. Made them for breakfast and my kids loved them. They are so soft, fluffy, and delicious. Thank you Olena!!
You’re welcome Kayla 🙂
I use Almond flour in my cooking. What ratio should I use when recipe says whole wheat flour please. Glenys
Almond flour and whole wheat flour are not interchangeable in baking. Here is my almond flour banana muffin recipes. You can add chocolate chips!
https://ifoodreal.com/almond-flour-banana-muffins/