Whole Wheat Banana Chocolate Muffins 

These muffins use applesauce and whole wheat flour to make your favorite banana chocolate chip muffin a little less sinful, but just as delicious.

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If you promise not to tell, no-one needs to know that these whole wheat banana chocolate muffins are just a little healthier for you than regular ol’ muffins. They are tender, moist and full of flavor and make a satisfying snack or dessert any day of the week. These muffins are based on this decadent and delicious banana bread recipe, but I’ve made a few wise substitutions to reduce the calorie count just a little. In that recipe, I talk about the importance of over-ripe bananas and how to ripen them quickly if you’re having an emergency craving. (FYI, to avoid having to quick-ripen the bananas, I always like to throw my bananas into the freezer as they start to over-ripen. Then, when I have three in the freezer I’m ready to make banana bread or muffins.) 

A bowl of mashed bananas with a fork, surrounded by a little bowl of apple sauce, two eggs and some melted butter.

How to Make Healthier Muffins

I’m not saying these muffins are diet food (trust me!), but it’s nice to know that you can substitute some of the ingredients for smarter choices and save yourself a few calories without sacrificing flavor. The first smart substitution is using a little unsweetened applesauce instead of sugar in the wet ingredients. Your muffins won’t taste like apples at all, but the natural sweetness from the applesauce is just enough to keep the muffins sweet and moist. 

Dry ingredients for banana muffins on a counter next to a square muffin pan.

Whole Wheat Muffins

Taking out some of the all-purpose flour and replacing it with whole wheat flour also helps with calorie count. By just substituting the applesauce and the whole wheat flour, you’ll save 80 calories per muffin (220 instead of 300). That’s worth it to me. Plus, the whole wheat flour gives you added nutrition and a density to the muffin that I like – it makes it more of a muffin and less of a cupcake.

A bowl of wet and a bowl of dry ingredients next to a square muffin pan.

Combining Wet and Dry

Mixing muffin batter is very straightforward. You combine all your wet ingredients in a bowl, combine all your dry ingredients in another bowl and then combine the two together, stirring only as much as you need to get the ingredients mixed so that no traces of dry ingredients can be seen. This is to ensure that you don’t over-mix the batter, which could result in tougher muffins. 

Banana Chocolate Muffin batter in a bowl with a red spatula.

The Right Muffin Pan

You can use whatever muffin pan you have, or even just muffin cups on a cookie sheet. I’ve used a square muffin pan here because I just happen to love this pan. I think square muffins are a nice change from the usual round muffin. Whatever you choose to use, make sure you butter the muffin cups – yes, even if they are non-stick. No-one likes to eat a muffin out of the pan. If you’re feeling decadent, you can even sugar the pan after you butter it. Add about a tablespoon of sugar to the cup and then shake it around and dump out any excess. This will give you a chewy exterior on the muffins.

Raw muffin batter in a square muffin pan.

Temperature is Key

The goal when baking muffins is to have a nice crown on top. The way to achieve a crowning muffin is to pop the batter into a hot oven and then drop the temperature after about 10 minutes, without opening the door. Not opening the door is key because you don’t want to let all the hot air out, just lower the temperature. The hot air at the start of baking gives the muffins a boost, but leaving it at such a high temperature for the duration of the cooking time would result in over-browned muffins. So, stick around when you put the muffins in the oven, do the dishes and then turn the oven down for the next 20 minutes.

Banana Chocolate Chip Muffins in a square muffin pan on a cooling rack.

How to Check for Doneness

The check for doneness on a muffin is the same as for a cake or quick-bread. Just pop a wooden skewer or toothpick into the center of one of the muffins in the center of the pan. It should come out clean with no batter. 

A close up of whole wheat banana chocolate muffins on a cooling rack.

How to Store Muffins

Although you’d think muffins would get more dry as they age, they actually become more moist first. The moisture, as it evaporates from the baked good, moves to the surface and the muffin can feel soggy. You can avoid this by storing muffins with some paper towel to absorb that migrating moisture. So, once the muffins have cooled completely, you should store them in an air-tight bag or container with some paper towel on the bottom. They can keep at room temperature for about 3 to 4 days. If you want to freeze muffins, wrap each cooled muffin in plastic wrap first and then place them in a zipper sealable plastic bag (or airtight container). They can keep in the freezer for 2 to 3 months.

A basket of muffins with two plates and two muffins, one broken open.

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Whole Wheat Banana Chocolate Chip Muffins

  • Prep Time: 10 m
  • Cook Time: 20 m
  • Total Time: 30 m
  • Servings:


  • butter to grease the pan
  • 3 very ripe bananas
  • 2 eggs
  • ½ cup applesauce unsweetened
  • 2 tablespoons melted butter
  • ½ cup white granulated sugar
  • ½ cup brown sugar
  • 1 cup all-purpose flour
  • ¾ cup whole wheat flour
  • ½ teaspoon baking soda
  • 1 teaspoon baking powder
  • ½ teaspoon salt
  • cups semi-sweet chocolate chips


  1. Pre-heat the oven to 425°Butter the inside of 12 muffin pan cups and set the pan aside.
  2. Mash the bananas with a fork in a large bowl. Add the eggs, applesauce, melted butter and sugar and mix until well combined.
  3. In a separate bowl, whisk together the all-purpose flour, whole wheat flour, baking soda, baking powder and salt. Add the dry ingredients to the wet ingredients and mix by hand, just until the dry ingredients are incorporated into the wet. Do not over-mix the batter. Gently fold in the chocolate chips.
  4. Fill the muffin cups ¾ of the way to the rim and transfer the pan to the middle rack in the oven.
  5. Bake at 425°F for 8 minutes. Then turn the oven temperature down (do not open the oven door at this pointo 350°F and bake for 10 to 12 minutes, until a toothpick inserted into the center of a muffin comes out clean.
  6. Transfer the muffin pan to a cooling rack and let it cool for 3 minutes. Then remove the muffins from the pan and cool completely on the cooling rack. (Run a butter knife around the edges if necessary, to loosen the muffins from the pan.)
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Comments (5)Post a Reply

  1. 5 stars
    Oh my these are delicious!! So moist and such a great texture. Definitely two thumbs up!! Thanks for another winning recipe! 🙂

  2. First time I’ve successfully made muffins. This will be a staple. One change, I used rolled oats (blitzed) instead of whole meal flour 👍🏼

    1. The applesauce is used instead of oil to keep the muffins moist without adding saturated fat. You can just use 1/2 cup of vegetable oil instead but it will change the nutritional value.

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