Greek Yogurt Choc Chip Muffins (Low Sugar Recipe)

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These Greek yogurt choc chip muffins are light and fluffy every time, packed full of protein and with only a little added sugar. They also happen to be REALLY quick and easy to make – ready in only 30 minutes.

Perfect for lunch boxes, afternoon snacks and last minute guests, you NEED these healthy chocolate chip muffins in your life!

Closeup of a Greek yogurt choc chip muffin on a pale beige plate and marble surface with more cakes and a striped blue tea towel behind.

Healthier chocolate chip muffins

We have a bit of a love-hate relationship with muffins in our house. Mr. Scrummy generally doesn’t like them, unless they happen to be these Greek yogurt blueberry muffins.

I certainly do like them, especially if they involve chocolate in any way, shape or form. However, I find café muffins mostly too sickly sweet.

My solution to this very serious problem (!) is to make these lower sugar light and fluffy Greek yogurt choc chip muffins at home. In my not-so-humble opinion, these are the best chocolate chip muffins ever (tongue slightly in cheek here, but they really are good muffins).

Why you’ll love them

Yes, Helen! You’ve discovered a healthy chocolate chip muffins recipe. Tell me all about it…

  • They’re light and fluffy with a lightly crispy top. Just like my blueberry muffins before them, these Greek yogurt choc chip muffins always seem to turn out well!
  • They are indeed healthier choc chip muffins than average. They’re protein-packed (hello Greek yogurt), and low in sugar with just 1⁄3 cup.
  • Ridiculously easy to make and hard to mess up. They’re made with oil, so there’s no creaming of butter and sugar. Just mix the wet ingredients into the dry. Perfect recipe for making with the kids!
  • Beautifully moist and tender since the oil and yogurt both add moisture.
  • Made with simple ingredients. You might already have everything in your pantry.
  • Chocolate chips in every bite! 😉

If this is going to call itself a chocolate chip muffin, it’s going to have plenty of chocolate chips in it.

5* Review

“Thank you SOOOO much for this recipe Helen! These turned out amazing and my husband and kids said they’re the best choc chip muffins they’ve ever had!” (Angie)

About the ingredients

Overhead view of all the ingredients needed to make Greek yogurt chocolate chip muffins including chocolate chips, eggs, milk, Greek yogurt, flour, baking powder, baking soda and salt, vanilla extract, oil and sugar.

As already mentioned, one of the great things about these choc chip muffins (that are on the healthier side!) is that you only need simple baking ingredients. I confess that I’ve not always been very accurate with the ingredient amounts, but they always turn out well.

Here’s what you need to know:

All-purpose/Plain flour: Nothing fancy here. Feel free to replace some of the white flour with white whole wheat flour, regular whole wheat (wholemeal) flour or gluten free flour. It works! You ‘may’ need to add a little extra milk with these alternative flours.

Baking powder and baking soda: You’ll add a whole tablespoon of baking powder since you’re using 2.5 cups of flour. Plus just a half teaspoon of baking soda.

Sugar: Just plain white sugar. 1⁄3 cup is enough for me since there are plenty of chocolate chips in the recipe for the perfect amount of sweetness. Feel free to increase the amount to ½ cup if you have a sweeter tooth.

Eggs: 2 large.

Oil: I usually use either canola oil, or a mixture of canola and light olive oil. Any vegetable oil, melted coconut oil or even melted butter would work, too.

Greek yogurt: A whole cup packs the protein into these muffins (protein muffins!). For the best results, always use authentic Greek yogurt which is just strained yogurt made of milk and yogurt cultures. Reduced fat (such as the blue Chobani) or full fat are both fine. Avoid the ‘Greek style’ yogurts that contain a lot of cream.

Milk: Just a little, to thin the batter to the right consistency.

Salt: Just half a teaspoon to bring out the other flavors.

Vanilla extract: Not essential, but just a teaspoon is nice.

Chocolate chips: I like dark, but milk is fine, too. I add a whole 1.5 cups for chocolate in every bite, but reduce this amount if you like. Feel free to use chocolate chunks instead of chips!

How to make them

The step-by-step guide below should help you make the recipe perfectly first time. Scroll down to the end for the full recipe including ingredient amounts.

Step 1: Preheat the oven and prepare the muffin tin(s) with paper liners. I also try to remember to spray the liners lightly with oil to stop them sticking.

Step 2: Stir together the dry ingredients in a large bowl – flour, baking powder and soda, salt, and the little bit of sugar.

Step 3: Stir together the wet ingredients – so eggs, oil, vanilla, yogurt, milk and vanilla if you like.

collage of 2 images showing Making  the batter for Greek yogurt chocolate chip muffins

Step 4: Briefly mix the wet ingredients into the dry (no overmixing!), and fold in the choc chips!

collage of 2 images showing stirring the choc chips through the batter for Greek yogurt choc chip muffins

Step 5: Fill the liners with the muffin batter. You’ll get 12 to 18 muffins depending on the size. Sometimes I make small muffins, other times huge bakery style ones. Both work really well!

Step 6: Bake until nicely browned! The baking time can vary. You’ll need between 17 to 25 minutes, again depending on the size. Check with a skewer in the middle. When it comes out clean, the delicious yogurt muffins are ready!

Overhead view of a pan of just baked Greek yogurt choc chip muffins on a marble background with a blue and grey striped tea towel at the top.

Helen’s top tips

To get perfect choc chip muffins every time!

  • Once you’ve added the wet ingredients to the dry, don’t overmix. A few lumps are fine! This will make sure you get light and fluffy muffins every time.
  • If your batter doesn’t drop nicely into your muffin cases and looks too thick and lumpy, just add a drizzle more milk to thin it out a bit.
  • Lightly fold your chocolate chips in. Again, don’t overmix and risk heavy, chewy muffins.
  • These muffins do tend to stick to the muffin cases a bit when still warm. If you wait until the muffins are completely cool they’ll peel out of the cases really easily. If you want to eat them warm, just reheat for 15 seconds in the microwave! (no longer – you’ll ruin them!)
A Greek yogurt chocolate chip muffin ripped open to expose the inside on a paper liner and with another muffin in the background.
Light and fluffy, moist, and with a crispy top

Variations

  • For even healthier chocolate muffins, reduce the chocolate chips to just ½ to 1 cup. Replace the rest with some fresh or frozen fruit – raspberries, blackberries or chopped pear (nice and sweet!) comes to mind.
  • Replace some of the chocolate chips with chopped nuts and/or dried fruit such as sultanas or cranberries.
  • I use almost exactly the same recipe for these Greek yogurt choc chip muffins as for my low sugar Greek yogurt blueberry muffins (they get rave reviews!). Except I add a little more sugar to the blueberry muffins to compensate for the lack of chocolate.

Recipe FAQ

How do you store these?

These yogurt muffins will keep well in an airtight container at room temperature for around 3 days, or in the fridge for around 5 days.

Can you freeze yogurt muffins?

Yes! You can freeze these Greek yogurt chocolate chip muffins in Ziploc bags for up to 3 months. Then defrost and reheat for 20-30 seconds in the microwave or a few minutes in the oven to get that freshly baked vibe again.

How can I make these dairy free?

Try making them with coconut Greek style yogurt. Check that it’s made with coconut milk and isn’t just coconut flavored yogurt. Remember to also replace the milk with a non-dairy milk such as almond, oat or soy.

Can I make mini chocolate chip muffins instead?

Yes, of course! Bake for just 10 to 13 minutes or until well risen and browned and a skewer pushed into the middle comes out clean. Check after 10 minutes and then if necessary every minute after that (a few minutes too long could ruin them).

Greek yogurt choc chip muffins on a white plate from above with more on a cooling rack in the corner

More favorite baking recipes

  • Here’s another go-to breakfast treat for you: delicious ooey, gooey 1-hour cinnamon scrolls. Try them once and they’ll become another favorite baking recipe!

Also check out this list of 25 low sugar cakes (that still taste great!).

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Closeup of a Greek yogurt choc chip muffin on a pale beige plate and marble surface with more cakes and a striped blue tea towel behind.
4.82 from 16 votes

Greek Yogurt Choc Chip Muffins (Low Sugar Recipe)

Welcome to your new favourite healthier chocolate chip muffins! These Greek yogurt choc chip muffins are really quick and easy to make, protein-packed, and quite low in sugar. They always seem to turn out well!
Prep: 10 minutes
Cook: 20 minutes
Total: 30 minutes
Servings: 12 to 15 muffins (depending on size)

Ingredients 
 

Dry ingredients

  • 2.5 cups plain flour
  • 1 tablespoon baking powder
  • ½ teaspoon baking soda
  • ½ teaspoon salt
  • cup sugar, I find this enough but some people might like to add a little more, say ½ cup sugar

Wet ingredients

  • 2 eggs, lightly whisked
  • cup oil, I usually use canola oil, or a mixture of canola and olive oil, but any is fine
  • 1 cup Greek yogurt, I use authentic full fat strained Greek yogurt
  • ¼ cup milk, Actually, ¼ to ½ cup.
  • 1 teaspoon vanilla extract, optional

Other

  • 1.5 cups chocolate chips

Instructions 

  • Pre-heat the oven to 355F/180C and line a muffin pan with muffin liners. Spray lightly with oil.
  • Combine the dry ingredients in a large bowl.
    2.5 cups plain flour, 1 tablespoon baking powder, ½ teaspoon baking soda, ½ teaspoon salt, ⅓ cup sugar
  • Combine the wet ingredients in a jug or smaller bowl.
    2 eggs, ⅔ cup oil, 1 cup Greek yogurt, ¼ cup milk, 1 teaspoon vanilla extract
  • Pour the wet ingredients into the dry and mix with a wooden spoon until just combined (a few lumps are fine. Don’t overmix). Add a little more milk if necessary (the mixture will be quite thick but it shouldn't be dry).
  • Gently fold the chocolate chips into the batter.
    1.5 cups chocolate chips
  • Spoon the batter into the muffin cases (you can fill almost to the top) and bake for 17 to 25 minutes. After 17 minutes keep checking every couple of minutes. A skewer pushed into the centre of the muffin should come out without raw batter on it, and the muffins should be nicely golden brown.
  • Let cool completely on a wire rack before eating so that the muffin cases don’t stick. Reheat for 15 seconds in the microwave after peeling off the muffin case if you’d like to enjoy a muffin warm!

Video

Notes

Batter consistency: Your batter should be a soft dropping consistency so you can put it into your muffin cases easily. If it seems too thick, just add a tiny bit more milk.
Baking time: The baking time can vary a bit depending on what brand of yogurt you use and/or how big your muffin cases are.
Just check every couple of minutes after 17 minutes until your muffins are nicely browned and a skewer pushed into the centre of a muffin comes out fairly clean (there might be a bit of chocolate on the skewer but there shouldn’t be any raw batter).
I’ve found cooking time to be as little as 17 minutes and as long as 25 minutes depending on the size of my muffins.
Storing and freezing: These muffins will keep quite well for a few days in an airtight container, but they also freeze well. Simply freeze in Ziploc bags or a plastic/glass container with a lid for up to 3 months. Defrost and then reheat for 15-20 seconds in the microwave or a few minutes in a warm oven.
Blueberry/Banana versions: You can easily make Greek yogurt blueberry muffins instead with this same recipe! Simply add a tiny bit more sugar to the batter (if you like – say 1/2 cup instead of 1/3 cup) and replace the choc chips with 1.5 cups of blueberries. 
Or make half chocolate, half blueberry muffins! Both are delicious and always turn out well.
If you have overripe bananas, you may also wish to try these Greek yogurt banana muffins (with caramel chips!). 

Nutrition

Calories: 365kcal, Carbohydrates: 42g, Protein: 6g, Fat: 18g, Saturated Fat: 4g, Cholesterol: 31mg, Sodium: 81mg, Potassium: 169mg, Fiber: 1g, Sugar: 20g, Vitamin A: 100IU, Vitamin C: 0.2mg, Calcium: 102mg, Iron: 1.7mg
Like this recipe? Rate and comment below!

About Helen Schofield

Don't expect to find anything fussy or complicated here. Just QUICK, EASY & (mostly!) HEALTHY recipes from the Mediterranean and beyond. ENJOY!

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82 Comments

  1. 5 stars
    Turned out amazing!! Approved by all the family!! Definitely my go to recipe for muffins from now on. Made them as mini muffins with brown sugar and half berries half choc chip. Yummo. Thank you for sharing

    1. Hi Yvonne, and thanks so much for the feedback. I’m very flattered that it’s now your go-to recipe. Thank you for letting me know! 🙂

  2. I have tried this recipe and the muffins turned out to be oily I wondered if I put to much in. I think. How much oil do I need like a cup? Or less.

    1. You need about two thirds of a US cup, Chelsy. Give them another go – they’re worth it!

    1. Hi Fion. I’ve made these muffins in several different kinds of ovens. I always stick to 180C but I find the cooking time varies quite a lot depending on how big the muffins are. I’d say just keep checking every couple of minutes after 25 mins until your skewer comes out of the cakes pretty clean. This recipe has never failed me so I hope they become a family favourite for you too! Merry Christmas!

  3. It is 2am here in Melbourne 🇦🇺 was craving chocolate chip muffin
    Just whipped those out and omg I’m gonna have an amazing sleep
    My house smells amazing
    My husband is gonna wake up and will definitely eat a few because they’re divine
    Thank you for sharing the recipe

    1. Hi Jennifer! So glad you’re doing so well over there in Melbourne now! And I hope your husband enjoyed the muffins as much as you thought he would! They’re pretty fail safe muffins, so I think so. You must try the blueberry version too!

      1. 5 stars
        Thank you so much for taking the time to reply

        Yes thank god after 7 months full lockdown depression with a new first born baby that was born 2 days before the crisis begun …. we are doing better now that the city is opening up slowly slowly thank god

        I hope you’re staying safe and looking forward to trying it with blueberries of course ❤️

      2. Ahhh, I can only imagine how difficult that’s been for you. Now that you’re doing so well over there I hope you can start going to some mother’s groups etc. You take care too! 🙂

  4. These are so nice! Super moist and loved by the adults and kids alike! I’m not against sugar but just in terms of school ( my daughters preschool is a big funny) has anyone tries them with honey?

    1. Hi Emilia – thank you so much for the feedback! I’m so glad you enjoyed these! I’m afraid I don’t remember anyone saying they replaced the sugar in these with honey, but I am quite confident that you could get away with replacing at least some of the sugar with honey. Try half and half and see how you go. I’ve been making this recipe for years (the blueberry ones in particular) and I find that they do very well with subsitutions! Good luck and if you get a chance please do let me know how you get on!

  5. 5 stars
    These muffins are so yummy! Choc chips in every bite! Definitely less sweet, which is nice.

    Thank you for sharing the recipe!

    1. Hello, and you’re so welcome! I’m so glad you enjoyed them. I feel like they have just the right level of sweetness with the added chocolate chips! 🙂

  6. Can I make these or your blueberry muffins with low-fat greek yoghurt, boysoy milk and all-purpose flour? (Just looking at things in my pantry!) Look forward to your reply, and eventually baking these!

    1. Hi Sarah! I think that will be absolutely fine! I find this recipe to be very forgiving i.e. you can make all kinds of substitutions and it usually works. Good luck!

  7. Hi,

    These look and sound great!
    Just wondering is it possible to substitute whole wheat flour for the plain flour?
    Also melted butter for the oil?
    Thanks

    1. Hi Aysha! Oh, definitely! I’ve made these with so many different substitutions and they always work out well. You ‘might’ need to add a tiny bit more milk if you use wholewheat flour, but see how you get on.

  8. Just made these muffins for my daughter and grandsons and had to sample one. Yum yum they are delicious and sooo easy to make. Will try blueberry next time.

    1. Oh thank you so much, Christine! You should definitely try the blueberry ones. If I had to choose I would probably choose the blueberry over the chocolate, and that’s coming from a total chocolate addict! 😉
      P.S. Oh, if you get a chance would be mind popping back to the recipe and giving it a rating? (just click the stars in the recipe card!) Thank you so much!

  9. 5 stars
    Helen, well done, another great muffin recipe!! 😋I’m taking them in tomorrow for my Infant’s health class as we’re doing a Healthy Living unit this term, and I make them a treat each week to show how low sugar can still be delicious…I’m positive they will love them, after all, choc chips…how can they not be awesome??!! BTW, I managed to get 17 reasonably good sized muffins. ⭐️⭐️⭐️⭐️⭐️

    1. Hi Rana! Oooh, I sincerely hope my son is lucky enough to get a teacher like you when he starts school! Thank you soooo much for feedback. I’m so glad the recipe seems to have worked out well for you, and well done for getting 17!! I’m thinking of you today – I really hope your beautiful kiddies enjoyed them!

      1. They did! It’s funny when six and seven year olds ask for the recipe 😋😋😋 love your work, keep it up! 👏🙏

      2. Oh that’s priceless! I love it! Thank you again, Rana. I love that you love this recipe! 🙂