Healthy Chocolate Chip Muffins
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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 πŸ˜‰ 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! πŸ˜€

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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