Healthy Chocolate Chip Muffins

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5 from 2 reviews

Simple Healthy Chocolate Chip Muffins made with whole grain flour and dairy-free too. This recipe is great for kids! 


  • 2 cups whole wheat pastry flour *(or 1:1 gluten-free all-purpose)
  • 2 tsp baking powder
  • 1/4 tsp salt
  • 1/2 cup oil (avocado, light olive, sunflower)
  • 1/3 cup maple syrup
  • 34 Tbsp granulated sugar, optional
  • 2 tsp vanilla extract
  • 2 large eggs, room temperature**
  • 2/3 cup non-dairy milk
  • 3/4 cup mini chocolate chips
  • coarse sugar for sprinkling tops


  1. Preheat oven to 425ºF. Grease 12 muffin cups or use silicone liners. Set aside.
  2. In a medium bowl whisk together flour, baking powder and salt. Set aside.
  3. In a large bowl whisk together oil with maple syrup, add in eggs and vanilla, whisk until combined. 
  4. Add bowl of dry ingredients into large bowl of wet ingredients. Gently begin to combine then add in milk and stir until ingredients are almost incorporated. Gently fold in chocolate chips, being careful not to over-mix. Batter will be somewhat thick. Avoid over-mixing the batter or you’ll end up with tough muffins.
  5. Evenly distribute batter into 12-cup muffin pan, filling 2/3 full (I like to use a medium cookie scoop). Sprinkle on more mini chocolate chips if you’d like and top with pinches of coarse sugar.
  6. Bake muffins at 425ºF for 5 minutes, then reduce oven temperature to 350ºF and continue baking for an additional 10-12 minutes, or until inserted toothpick in center of muffin comes out clean. Allow muffins to cool in pan for about 10 minutes before gently removing. TIP: if greasing muffin pan, I use a butter knife to remove from pan.
  7. Transfer chocolate chip muffins to wire rack and allow to cool completely before storing. Muffins are best enjoyed fresh within 3 days. These muffins are a little bit more dense than traditional muffins but still delicious! They taste amazing warmed up with a little bit of butter.



*FLOUR  – Whole wheat white flour OR half all-purpose half whole wheat flour OR 1:1 gluten-free all-purpose flour will be fine. I did not test with grain-free flours. If looking for grain free muffins, try these.

*TO MAKE VEGAN – Sub eggs with 2 Tbsp flaxseed meal + 1/3 cup water; let mixture gel up for 5 minutes. I haven’t tested the egg free version with the 1:1 gluten free flour, so if trying this way, the results may differ.

Feel free to half the batch if you’d like less muffins.

recipe slightly updated in 2021 for better results and vegan version.