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Healthy Chocolate Chip Muffins

Healthy Chocolate Chip Muffins

Who wants a muffin? How about a super high Healthy Chocolate Chip muffin with a perfect muffin top. And by perfect I mean, nice an’ tall, slightly crispy on the outside, soft on the inside and full of melty chocolate chips kinda muffin.

One disappointment I’ve always had with homemade muffins is that they are never as high as the ones sold at the bakery. And we all know the muffin top is the best part, right?!

chocolate chip muffins

And these Healthy Chocolate Chip Muffins do not disappoint 😉 They are based off one of my favorite loaves on this blog – my Chocolate Chip Quick Bread. And I gotta tell you guys, these muffins, straight out of the oven, warm and ooozing with chocolate chips and vanilla flavour is pure muffin bliss.

Plus, these Vegan Chocolate Chip Muffins are much healthier than traditional bakery muffins. You could say these are *bakery style* muffins just a whole lot better for you. These muffins are completely oil-free and made with my preferred flour of choice for all my healthy baking – Spelt Flour. You can read a bit more about why I love baking with Spelt Flour here.

healthy chocolate chip

Here are a few tricks to get these Super High Chocolate Chip Muffins just perfect:

1/3 heaping cup of muffin batter in each muffin cup: This step ensures that these muffins form killer muffin tops in the oven. This means that each muffin cup should be filled just shy of the top of each muffin cup. 

1 entire tablespoon of vanilla extract for maximum flavor: Extra vanilla adds such depth to these healthy muffins. I know this seems like a lot of vanilla extract but I would only recommend skimming it back a bit if you are sensitive to the vanilla flavor in baking.

Mini Chocolate Chips: Does this even need ‘splaining? Because mini chocolate chips are the cutest and mini pieces of chocolate means more chocolate chips spread into each muffin and more chocolate in each bite. Yum. These are my go-to allery-friendly chocolate chips I used in these muffins. They are certified vegan and gluten-free.

Baking in a very hot oven for the first 5 minutes: This makes sure your muffins pop up during the initial baking time, there are no taking chances with getting the perfect muffin tops around here! 😀

Happy Baking!

Healthy Chocolate Chip Muffins


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Healthy Chocolate Chip Muffins

  • Author: Ceara
  • Total Time: 32 mins
  • Yield: 9 muffins 1x


These Healthy Chocolate Chip Muffins are just like the muffins you get at the bakery. They are made with a super high muffin top, are crispy on the outside and soft, ooey-goeey and full of melty chocolate chips on the inside. These muffins are 100% oil free, refined sugar free and made with spelt flour.



Wet Ingredients

  • 1 flax egg (1 tbsp ground flax seed + 3 tbsp water)
  • 1/2 tbsp white or apple cider vinegar
  • 1 cup almond or soy milk
  • 1 tbsp vanilla extract
  • 1/3 cup applesauce
  • 1/2 cup cane sugar + 2 tbsp to sprinkle on top

Dry Ingredients

  • 2 cups white spelt flour
  • 3 tsp baking powder
  • 1/2 tsp sea salt
  • 1/4 tsp nutmeg
  • 3/4 cup mini chocolate chips + 2 tbsp to sprinkle on top


  1. Pre-heat the oven to 425F/220C. Oil the muffin pan with coconut oil or cooking spray (so the muffins won’t stick!).
  2. Add flax and water to a large mixing bowl. Stir around and leave to sit for a couple minutes until it has thickened and formed an egg-like consistency. In a small bowl, while the flax egg is thickening, mix the almond milk and vinegar together and leave to sit for a couple minutes (this forms a vegan “buttermilk”).
  3. Once the flax egg is thickened, add the remainder of the “wet” ingredients (milk mixture, vanilla extract, applesauce and cane sugar) to the large bowl and whisk until fully combined.
  4. In a medium size bowl, add the dry ingredients (spelt flour, baking powder, sea salt, nutmeg and chocolate chips) and mix together until the ingredients are evenly dispersed.
  5. Whisk the wet ingredients into the dry ingredients in the large mixing bowl. Make sure to not over-mix – it’s okay if there is a couple lumps in the batter like pancake battter.
  6. Pour 1/3 cup of the muffin batter into each cup of the muffin pan (or to almost the top of each muffin cup). Sprinkle additional chocolate chips and cane sugar on top of each muffin and bake for 5 minutes at 425F/220C. Lower the heat to 375F/190C, leaving the muffins in the oven until they are fully baked (14 – 18 minutes). The muffins are fully baked when an inserted toothpick comes out clear. The amount of time your muffins will need to bake will depend on your oven, mine took a total of 20 minutes. Once baked, leave the muffins to cool in the pan for 5 minutes before removing to cool on a cool rack or plate! Enjoy!


1)Sub spelt flour for white whole wheat or all purpose flour
2) Replace cane sugar with coconut sugar or with normal/light brown sugar – recipe will no longer be refined sugar free if replacing with normal/light brown sugar.

  • Prep Time: 12 mins
  • Cook Time: 20 mins
  • Category: Dessert
  • Cuisine: American

ceara s kitchen

If you try these Healthy Chocolate Chip Muffins, I LOVE seeing your delicious #CearasKitchen creations. Share your photos with me on Instagram @CearasKitchen (and remember to tag #CearasKitchen so I don’t miss it!) or share it on my Ceara’s Kitchen Facebook page. Wishing you a wonderful weekend!

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  1. Your passion for writing is truly contagious! Your article not only informed me but also ignited my own creativity. Looking forward to more of your insightful pieces

  2. Hi! These look great! I’ve had trouble baking with apple sauce in the past, can you taste it in this recipe?

    Thanks so much in advance!

  3. I don’t have enough chocolate chips on hand. Could I use frozen blueberries? Or would it make them mushy?

  4. Yummy, yummy! These muffins were a bit too good! I could not stop eating them. Good thing, I cut the recipe in half. I need to try them again, when I have better control. I had to use cashew milk and white flour, as that is what I had on hand. I did have the cane sugar (surprise to me!) and the rest of the ingredients.

  5. These worked out SO WELL for me! Both my family and I loved them. They were so moist and FLUFFY. I’ve never gotten the chance to use vegan buttermilk before, so it was so fun to get the chance to try. Thanks for the awesome recipe.

  6. Hi,
    I just saw your recipe and really want to give it a shot. Do you know if all-purpose flour could be used instead of white splet flour?

  7. I used mashed warmed bananas instead of applesauce and subbed 1/2 cup of the spelt for almond flour, it came out very rich but still fluffy like a bakery muffin; )

  8. Can you recommend a substitute for the apple sauce? I don’t have any on hand! Also would 1 regular egg work instead of the flax egg?

    1. Hi Krista,

      I am not sure how this recipe would work without the applesauce since it is what makes this bread so moist and soft without any oil. I’ve also only made these muffins with flax eggs – I imagine a “chia” egg would also work (replaxing the flax seeds, 1 for 1 with chia seeds!).


  9. I made these for the first time tonight, and I was thrilled with how they turned out! I’m currently trying to lose weight (16 pounds off so far) and I’m kind of addicted to those enormous chocolate chip muffins one buys at the bakery, but haven’t been able to have that kind of thing on my food plan.

    Needless to say, I was really happy to find a much lower-calorie/lower-calorie recipe for muffins that taste just as good as the ones from the bakery. This recipe is going into my repertoire, for sure.

    1. Yay!! So happy you enjoyed the muffins, Chloe! 🙂 Thank yous so much for the lovely feedback. And congratulations on your journey towards health!!

  10. I only have white sugar or dark brown sugar. Which would work best? Totally in the mood for these- they look amazing!!

  11. Thanks for sharing this recipe. I have been experimenting with muffin recipes and they are too oily. I don’t feel good after eating them. But these were delicious. They satisfy my sweet tooth without having to feel guilty for eating too much oil.

  12. do you think oat flour will work well? ask do you happen to know the nutritional stats for this recipe?

    1. I don’t think oat flour would work well in this reicpe. It would produce a very dense muffin. If you’d like a chocolate chip recipe using oat flour you could give this one a go –> http://www.cearaskitchen.com/healthy-chocolate-chip-banana-bread-bars/. You could even try baking them in muffin tins if you are looking specifically for a muffin recipe. Happy Baking!

      And you can plug the ingredients into here for the nutritional info –> http://www.caloriecount.com/cc/recipe_analysis.php

    1. Thanks SO much girl! I really appreciate it and all your photo advice over our chat!! Food photography is SUCH a learning curve but it’s so much fun! 🙂

  13. I saw these on FB and fell in love with there little chocolate-speckled sugar-sprinkled adorable selves! You made some great points about the mini chips: more chocolate, more cuteness, I need to make the switch to mini 🙂

    1. I’m so in love with adorable mini chocolate chips right now in my baked goods! <3 Thanks so much, Natalie!!

  14. I was wondering if these were based off your yummy chocolate chip bread and I was right!! YUM! They are just gorgeous and I cannot stand the concave, sad looking muffins I see so often around the internet. You know, the dense, squishy ones with no rise at all. For me, muffins should look both gorgeous AND taste amazing…especially since we eat with our eyes first. SO I am loving that these are super gorgeous and fluffy! I have some on my blog that I make that are gluten-free that get super fluffy too and they are delicious but yours are more low-fat since I use almond flour, so I could still eat your version and wear a swimsuit, lol! I’ll definitely have to try these next time!

    1. Concave muffins = the worst!!! Give me sky-high muffins and I’m happy 😉 Thanks so much, Brandi!! I just ordered some more almond flour and am going to try your chocolate muffins next! I’m drooling over how delicious they look 🙂

        1. Hi Al, if you put the ingredients into this site you’ll get the nutritional info! caloriecount.about.com/cc/recipe_analysis.php

          🙂 Enjoy the muffins!

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