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Healthy banana muffins with applesauce and chocolate chips make a great nutritious breakfast or snack option. There are so many recipes that use applesauce, and this is one of my favorites!

They’re not just delicious, they’re a sneaky way to add some extra nutrition to your breakfast or afternoon snack. This recipe keeps things naturally sweet with mashed bananas, unsweetened applesauce, and a touch of raw honey. No refined sugar here, just pure goodness. These are some of our favorite best healthy muffin recipes.

But these muffins are more than just a sweet treat. They’re also gluten-free! I’m swapping out all-purpose flour for millet flour, a nutrient-rich grain that adds a delightful nutty texture and keeps everyone at the table happy. So go ahead, and indulge in a guilt-free muffin (or two) – your taste buds and your body will thank you.

Take your healthy muffins to the next level with homemade applesauce. Not only does it add natural sweetness, but it also allows you to control the ingredients and ensure a perfectly customized flavor for these delicious treats.

What You Need to Make Healthy Banana Muffins with Applesauce

You only need a few simple ingredients to make this healthy recipe. You can find most of these items at the local grocery store, Whole Foods, or online. 

• 3 overripe bananas, mashed
• 1/2 cup applesauce
• ​2 eggs, room temperature 
• 1/3 cup honey
• 2 Tbsp coconut oil
• 2 cups millet flour
• 1 tsp vanilla bean powder
• 1 Tbsp baking powder
• 1 tsp baking soda
• 1/2 tsp sea salt
• 1/2 cup dark chocolate chips, plus more for the tops

Ingredients Tips and Substitutions

Check out our guide to healthy baking essentials for gluten-free kitchens! It’ll ensure you have everything on hand to whip up these delicious muffins and many other gluten-free treats.

Forget the picture-perfect yellow banana. When it comes to baking, brown bananas, or bananas with plenty of brown spotsoffer the most sweetness. As bananas ripen, their starches convert to sugars, making them not only sweeter but also adding a deeper, more complex flavor to your baked goods.

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​Vanilla bean powder is a pure form of vanilla, made from ground vanilla beans. If you don’t have vanilla powder, you can use vanilla extract. For 1 vanilla bean powder, you would use 2 tsp of vanilla extract. 

For the chocolate chips, I opt for the decadent and healthy twist of dark cacao chips. These gems are typically dairy-free and boast a high cacao content, around 85% in this case. This translates to a richer, purer chocolate flavor with less sweetness.  

This healthy banana chocolate chip muffins recipe is flexibleYou can use store-bought applesauce for convenience, or take your muffins to the next level with homemade applesauce. Check out my easy applesauce recipe for a perfectly customized flavor.

You also need a muffin pan, hand mixer, and muffin liners to make this healthy banana muffin recipe. I love these parchment paper liners.

How to Make Easy Banana Muffins with Applesauce

First, preheat the oven to 350 degrees F.

Then in a large bowl combine the mashed bananas and the eggs.

Next, add the applesauce to the bowl. 

Add the raw honey to the applesauce mixture. If you don’t have honey, you can use maple syrup. These are both great natural sweeteners for healthy banana applesauce muffins. 

Add the coconut oil to the bowl.

Next, add the millet flour to the wet ingredients. Millet flour is a naturally gluten-free flour made from finely ground millet seeds. It is a great substitute for all-purpose flour in many gluten-free baking recipes. It adds a nice touch of nuttiness and a slightly crumbly texture to baked goods.

Then add the rest of the dry ingredients: baking powder, baking soda, salt, and vanilla powder.

For a quick and easy mix, grab your hand mixer and combine the muffin batter until incorporated.

Mix until smooth. Then gently fold the dark chocolate chips into the batter.

How Long to Bake Healthy Banana Applesauce Muffins

Line the muffin pan with paper liners, then use a ¼ cup measuring cup to evenly distribute batter among the muffin cups for perfectly portioned muffins.

Then sprinkle a few more chocolate ships on the tops of the muffins and place in the preheated oven for 18-20 minutes. 

Remove the applesauce banana muffins from the oven when they pass the toothpick test. Transfer the muffins to a wire rack to cool.

Healthy Gluten Free Banana Applesauce Muffins

These wholesome and nutritious muffins are a great recipe for a guilt-free easy breakfast or afternoon cravings.

Forget overly sweet treats, these are a better choice. They’re packed with natural sweetness from bananas, applesauce, and a touch of honey. They’re perfectly balanced and refined sugar-free. Plus, they’re gluten-free thanks to nutty millet flour.

The slightly dense texture is ideal for dunking in your morning coffee or tea, making them a satisfying way to start your day. Incredibly flexible, use store-bought applesauce for convenience or homemade for a customized touch. Don’t forget the dark chocolate chips for a rich, pure chocolate flavor. These muffins are sure to become a new family favorite.

These muffins are perfect for portion control. Store leftovers in an airtight container at room temperature for a few days, or freeze them for a longer-lasting treat. They thaw and reheat easily in the microwave.

More Recipes that Use Applesauce

• Applesauce Coffee Cake Loaf
• Chocolate Chip Cookie Recipe with Applesauce
• Healthy Blueberry Oatmeal Muffins with Applesauce

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