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Banana Chocolate Chip Muffins (with whole wheat and quinoa flour)

These healthier Banana Chocolate Chip Muffins made with whole wheat and quinoa flour are perfect for breakfast or a mid-afternoon snack.

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Banana Chocolate Chip Muffin on dish with basket of muffins in background.

I've made this whole wheat and quinoa flour banana chocolate chip muffin recipe so many times now and the muffins always bake up beautifully. The muffins are light, moist, fluffy, filling and have just the right amount of sweetness.

Banana Chocolate Chip Muffins in muffin pan.

This is one of those recipes that has great flexibility with ingredients. I've had success using a combination of all-purpose or whole wheat pastry flour with oat or quinoa flour. The recipe I'm sharing with you here combines whole wheat pastry and quinoa flour.

Using whole wheat and quinoa flour is often my way of increasing the nutrition in baked goods such as muffins and cookies. Quinoa is an excellent source of protein, so using quinoa flour helps to increase the amount of protein in the muffins which in turn helps you feel full longer.

Banana chocolate chip muffin on dish.

How to Make these Banana Muffins

The muffin batter is easy to prepare and there are a few substitutions you could make if you don't have all the ingredients on hand.

Overview of Ingredients:

  • Whole wheat pastry flour
  • Quinoa flour
  • Baking soda and salt
  • Ground Cinnamon and Nutmeg. There's a touch of ground nutmeg in this recipe, you could simply omit it if you don't have any.
  • Granulated sugar, you can substitute brown sugar. I haven't tried the recipe with coconut sugar but I don't see a reason why it wouldn't work. Do let me know in the comments if you give it a try!
  • Yogurt or sour cream, I've had great success with both.
  • Light tasting oil
  • Eggs
  • Pure vanilla extract
  • Bananas, medium-sized
  • Mini semi-sweet chocolate chips. If you don't have any chocolate chips on hand you could substitute with nuts if allergies aren't a concern. Half a cup to three-quarters of a cup of chopped walnuts or pecans would be delicious.
Banana Muffin on dish.

Store the muffins in an airtight container on the countertop for up to 3 days and then store any leftovers in the refrigerator. Muffins can also be frozen up to three months.

Next time you have the urge to bake give these banana chocolate chip muffins a try, I'm sure you'll be happy you did.  Enjoy!

More Delicious Banana Muffins

Banana Chocolate Chip Muffin on dish with basket of muffins in background.

Banana Chocolate Chip Muffins (with whole wheat and quinoa flour)

Sweet and Savoury Pursuits
These simple to make delicious Banana Chocolate Chip Muffins are perfect for breakfast on the go or for a mid-afternoon snack.
4.75 from 8 votes
Prep Time 12 mins
Cook Time 18 mins
Total Time 30 mins
Course Breakfast, Snack
Cuisine American
Servings 12 muffins
Calories 293 kcal


  • 1-1/4 cup whole wheat pastry flour
  • 3/4 cup quinoa flour
  • 1 teaspoon baking soda
  • 1/2 teaspoon ground cinnamon
  • 1/4 teaspoon sea salt
  • 1/8 teaspoon nutmeg
  • 3/4 granulated sugar
  • 1/2 cup yogurt I used Balkan Style
  • 1/3 cup light tasting oil
  • 2 eggs
  • 1 teaspoon pure vanilla extract
  • 3 bananas mashed, medium sized
  • 2/3 cup mini semi-sweet chocolate chips


  • Place a rack in the centre of your oven and preheat oven to 375ºF.
  • In a large bowl, combine the whole wheat pastry flour, quinoa flour, baking soda, salt, cinnamon and nutmeg.
  • In a separate bowl, add the sugar, oil, yogurt, eggs, vanilla extract and mashed bananas, whisk together until well combined.
  • Add the wet mixture to the dry ingredients and fold batter with rubber spatula until just combined.
  • Add the chocolate chips and fold in. Don't over-mix the batter or you will have tough muffins.
  • Spoon the batter into the greased or paper-lined muffin cups distributing the batter evenly over 12 muffin cups.
  • Bake at 375ºF for 5 minutes and then reduce heat to 350ºF and continue to bake for 13 to 15 minutes more. To test for doneness, insert a toothpick in the centre of a muffin, if it comes out clean or with a few crumbs the muffins are done.
  • Remove the muffins from the oven and let them cool in the pan on a rack for 5 minutes.
  • Remove the muffins from the pan and place onto a wire rack to cool.
  • Store the muffins in an airtight container at room temperature for two to three days. For longer storage keep in the fridge or you can also freeze them for later consumption.


Calories: 293kcalCarbohydrates: 40gProtein: 5gFat: 13gSaturated Fat: 3gCholesterol: 29mgSodium: 171mgPotassium: 251mgFiber: 3gSugar: 21gVitamin A: 75IUVitamin C: 2.6mgCalcium: 33mgIron: 1.8mg
Keyword Banana Chocolate Chip Muffins, Quinoa Flour Banana Muffins, Whole Wheat Banana Muffins
Tried this recipe? Have any questions, comments or suggestions? Leave a comment below!Mention @sweetandsavourypursuits or tag #sweetandsavourypursuits!


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