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+ servings
Two halves of a chocolate banana muffin on a plate.

Healthy Chocolate Banana Muffins

These Healthy Chocolate Banana Muffins are packed full of nutrition and flavor. Feel good about feeding your family these for a quick breakfast!
4.92 from 12 votes
Yield: 17 muffins
Prep Time:20 minutes
Cook Time:17 minutes
Total Time:37 minutes

Ingredients
 

  • 3/4 cup all-purpose flour
  • 3/4 cup whole wheat flour (I prefer white whole wheat.)
  • 1/3 cup sugar (I like coconut sugar, since it has more nutrients.)
  • 1/4 cup ground flaxseed (sub: flour)
  • 1/4 cup cocoa powder
  • 1 teaspoon baking soda
  • 1/4 teaspoon baking powder
  • 1/2 teaspoon salt
  • 1/2 teaspoon cinnamon
  • 2 medium bananas (ripe and mashed well; about ¾ cup per batch)
  • 1/2 cup pureed pumpkin (sub: sweet potato puree)
  • 1/2 cup avocado oil (sub: another neutral oil)
  • 1/3 cup nonfat plain Greek yogurt
  • 1/3 cup honey
  • 2 large eggs (beaten)
  • 1 1/2 teaspoons pure vanilla extract
  • 2/3 cup mini semi-sweet chocolate chips

Instructions
 

  1. Prep: Preheat oven to 350°F. Grease a standard muffin tin or line with silicone or paper liners. (Note: Silicone liners will increase bake time by a few minutes.)
  2. Dry Ingredients: In a large bowl, whisk together the flours, sugar, ground flaxseed, cocoa powder, baking soda, baking powder, salt, and cinnamon.
  3. Wet Ingredients: In a medium bowl, whisk together the mashed bananas, pumpkin purée, avocado oil, yogurt, honey, eggs, and vanilla until combined. (Tip: Blend all this in a small blender to avoid any chunks.)
  4. Combine: Add the wet ingredients to the dry ingredients and stir just until a few streaks of dry ingredients remain. Gently fold in the chocolate chips, stirring only until all dry ingredients are incorporated. Do not overmix.
  5. Bake: Scoop about ¼ cup of batter into each prepared muffin cup. Bake for 17-22 minutes, or until a wooden toothpick inserted into the center comes out clean.
  6. Cool and Enjoy: Remove from the oven, carefully transfer muffins from the pan to a wire rack, and allow to cool completely.

Freezer Instructions

Freeze for Later: Bake muffins according to the directions. Place the cooled muffins on a cookie sheet lined with parchment or wax paper and flash freeze until firm. Once frozen, transfer the muffins to a freezer-safe bag or container. Store for up to 3 months.
Prepare from Frozen: Thaw muffins at room temperature or in the refrigerator. For a quick option, warm them briefly in the microwave before serving.

Notes/Tips

  • Don’t over-mix the batter. To keep them light and fluffy, only mix the batter to the point where all the dry ingredients are combined.
  • Use ripe bananas for the best flavor. The bananas bring a lot of sweetness to this recipe so make sure they are nice and ripe!
  • Store muffins in an airtight container or ziploc bag at room temperature for 2-3 days, or in the refrigerator for 3-5 days.
  • We updated this recipe in January 2026. If you are looking for the original recipe, you can download it here.

Nutrition

Serving: 1 muffin | Calories: 226 kcal (11%) | Carbohydrates: 28 g (9%) | Protein: 4 g (8%) | Fat: 12 g (18%) | Cholesterol: 23 mg (8%) | Sodium: 152 mg (7%) | Fiber: 3 g (13%) | Sugar: 15 g (17%)
If you make this, please leave a review and rating letting us know how you liked this recipe!