stack of healthy chocolate chip muffins on tea towel
How to Make...

Simple Healthy Chocolate Chip Muffins

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

  • Prep Time: 10 minutes
  • Cook Time: 20 minutes
  • Total Time: 30 minutes
  • Yield: 12 muffins 1x
  • Scale:


  • 2/3 cup non-dairy milk
  • 1/2 TBS apple cider vinegar
  • 2 cups whole wheat pastry flour *(or 1:1 gluten-free all-purpose)
  • 3/4 tsp baking powder
  • 1/2 tsp baking soda
  • 1/2 tsp salt
  • 1/3 cup + 1 TBS oil (avocado, sunflower, or liquid coconut)
  • 1/3 cup maple syrup
  • 1/2 tsp vanilla
  • 1 large egg**
  • 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 glass measuring cup add 2/3 cup of milk + ½ TBS of apple cider vinegar, set aside for about 5 minutes.
  3. In a medium bowl whisk together flour, baking powder, baking soda, and salt. Set aside.
  4. In a large bowl whisk together oil with maple syrup. Add in egg and vanilla and whisk until combined. Pour milk-vinegar mixture and gently stir.
  5. Add bowl of dry ingredients into large bowl of wet ingredients. Using large spatula gently combine until all dry ingredients are almost incorporated.
  6. 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.
  7. Evenly distribute batter into 12-cup muffin pan, filling 2/3 full (about ¼ cup of batter). Sprinkle on more mini chocolate chips if you’d like and top with pinches of coarse sugar.
  8. Bake muffins at 425ºF for 5 minutes, then reduce oven temperature to 375ºF and continue baking for an additional 10-15 minutes, or until inserted toothpick in center of muffin comes out clean. Allow muffins to cool in pan for about 10-15 minutes before gently removing. TIP: if greasing muffin pan, I use a butter knife to remove from pan. 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 so I’d suggest warming them up to help soften.

Recipes Notes:

*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.

*TO MAKE VEGAN – Sub egg with 1 TBS flaxseed meal + 3 TBS water; let mixture gel up for 5 minutes.

Nutrition Information:

  • Serving Size: 1 muffin
  • Calories: 223
  • Sugar: 14
  • Sodium: 194
  • Fat: 11
  • Saturated Fat: 8
  • Unsaturated Fat: 0
  • Trans Fat: 0
  • Carbohydrates: 28
  • Fiber: 3
  • Protein: 4
  • Cholesterol: 16