Easy Chocolate Banana Muffins With Freshly Milled Flour
Fresh milled chocolate banana muffins are the most delicious (and nutritious!) little treats around with the health benefits of whole grains and the sweet taste of chocolate. The tender crumb of fresh milled flour pairs perfectly with overripe bananas and rich chocolate for a muffin that everyone will love! Hearty texture, indulgent chocolate, and an easy to make snack – all in one recipe!

Everyone loves banana chocolate chip muffins, and these whole wheat flour ones are simply the best around. The natural sweetness of the bananas pairs perfectly with the slightly nutty flavor of whole grain flour and the rich indulgence of cocoa powder. Add in a few chocolate chips, and you have the perfect muffin recipe.
Not only are these muffins delicious, but they freeze well. We always make a batch and freeze half. Then we can have the best chocolate banana muffins anytime! It’s a great way to get a quick breakfast on the table on busy mornings or throw together a quick snack.
Pair these perfectly fluffy muffins with a high protein breakfast casserole (both of which you can make ahead!) or sausage balls anytime you need an easy meal or a quick energy boost.
While these chocolate chip banana muffins are an all time favorite around here, we also love to make fresh milled blueberry muffins and kodaik cakes banana bread for simple, nutritious snacks.
If you’re new to baking with freshly milled flour, check out the baking with whole wheat guide and our favorite everyday fresh milled bread recipe!

Why You’ll Love This Recipe
Simple recipe. All you need are some pantry staples to whip up this recipe anytime you want a sweet, nutritious treat!
Big flavor. The natural sweetness of bananas pairs perfectly with the nutty nutrition of fresh milled flour. Add in cocoa powder and chocolate chips, and you have a healthy recipe with tons of flavor.
Nutritious and delicious. Most chocolate muffin recipes are lacking in nutrients, but because we’re using whole wheat flour that’s milled right before baking, we get all the vitamins (vitamin e, b, d, a, and more!), protein, fiber, and minerals.
What are Fresh Milled Chocolate Banana Muffins?
Fresh milled chocolate banana muffins are a healthier take on the classic chocolate chip banana muffin. Using freshly ground whole wheat flour, these muffins have more vitamins and minerals than those that use store-bought flour. Because freshly milled flour contains both the bran and germ, it is considered healthier. This also gives the muffins a richer taste.
Whole wheat chocolate banana muffins are moist and rich with the mashed banana, cocoa powder, and chocolate. Many recipes use sourdough starter, leftover sourdough discard, or sour cream to achieve a moist consistency. And while we love sourdough banana muffins, this recipe doesn’t need that!

Fresh Milled Chocolate Banana Muffins Ingredients
- Fresh milled soft white wheat flour: Soft white wheat berries work best for recipes like this, and we love to mill our own flour. You can also use store-bought flour or even all-purpose flour. I get my wheat berries from Azure Standard.
- Melted butter: Butter gives the most moist crumbs and makes an oil-free muffin. You can also use coconut oil or avocado oil to make these muffins dairy-free. Olive oil would impart too much flavor, so I would avoid it.
- Maple syrup: When working with freshly milled flour, I tend to use liquid sweeteners as the flour absorbs more liquid. You could use something like coconut sugar or brown sugar, but it would change the texture.
- Chocolate chips: You can really use any that you like, but milk chocolate will make these muffins very sweet. I usually mix 1/2 cup semi-sweet and 1/2 cup dark.
A full list of ingredients and quantities can be found in the recipe card below.
Tools You May Need
- Grain mill: Milling your flour is one of the first things you’ll need to do for this recipe. I love my Komo that I got off Marketplace. The Nutrimill is also a wonderful option.
- Muffin pan: We make a mix of mini muffins and regular size. For the mini ones, cut the baking time in half.
- Ice cream or cookie scoop: This just makes spooning into muffin cups easy! You can also use a spoon.

How to Make Fresh Milled Chocolate Banana Muffins
- Preheat your oven to 350 degrees and line the muffin cups with paper liners or spray them with oil. Set aside.
- Mill your soft white wheat into flour. It takes a bit over 1 cup of wheat berries to get 1 & 1/2 cups of flour.
- In a large mixing bowl, mash the bananas well with a fork. Then add the wet ingredients to the mashed bananas – maple syrup, egg, butter or oil, and vanilla. Mix until well combined. You an also use a stand mixer, if desired.
- Stir the dry ingredients together in a separate bowl – the freshly milled flour, then the baking powder, baking soda, and salt. Then add to the wet ingredients.
- Fold in the chocolate chips until just mixed through the batter.
- Use an ice cream scoop or large spoon to spoon the muffin batter into the prepare muffin tin. Fill each liner about 3/4 way to the top.
- Bake on 350 degrees for 20 minutes or until a toothpick inserted into the muffin comes out clean.
- Let your muffins cool in the pan for about 10 minutes, then transfer to a wire rack to cool. This prevents the bottom from holding too much moisture. Serve on their own or with a dollop of peanut butter.
- Once completely cooled, store leftover muffins in an airtight container at room temperature for up to two days. Transfer to the fridge to extend the shelf life.


Recipe Tips
- Use spotty bananas: The riper the bananas, the sweeter and more flavorful your muffins will be.
- Mill flour fresh: Grind your wheat berries right before baking to preserve nutrients and the best flavor.
- Don’t over-mix: Once you add the dry ingredients, stir just until combined to keep the muffins light and tender.
- Scoop evenly: A cookie or ice cream scoop helps portion the batter so all muffins bake evenly.
- Cool completely: Letting them cool on a wire rack prevents soggy bottoms and helps the chocolate chips set.
Recipe FAQs
I hope you love this recipe!
Whole Wheat Banana Chocolate Muffins with Freshly Milled Flour
Ingredients
- 3 ripe bananas
- 1/2 cup maple syrup
- 1 egg
- 1/4 cup melted butter or avocado oil
- 1 teaspoon vanilla extract
- 1 & 1/2 cups fresh milled soft white wheat flour
- 1/2 cup unsweetened cocoa powder
- 1 teaspoon baking powder
- 1 teaspoon baking soda
- 1/2 teaspoon salt
- 1 cup miniature semi-sweet chocolate chips or a mix of semi-sweet and dark
Instructions
- Preheat your oven to 350 degrees and line the muffin tins with paper liners or spray. Set aside.
- Mill your soft white wheat into flour. It takes a bit over 1 cup of wheat berries to get 1 & 1/2 cups of flour.
- In a large mixing bowl, mash the bananas well with a fork. Then add the wet ingredients to the mashed bananas - maple syrup, egg, butter or oil, and vanilla. Mix until well combined.
- Stir in the dry ingredients - the freshly milled flour, then the baking powder, baking soda, and salt.
- Fold in the chocolate chips until just mixed through the batter.
- Use an ice cream scoop or large spoon to spoon the muffin batter into the prepare muffin tin. Fill each liner about 3/4 way to the top.
- Bake on 350 degrees for 20 minutes or until a toothpick inserted into the muffin comes out clean.
- Let your muffins cool in the pan for about 10 minutes, then transfer to a wire rack to cool. This prevents the bottom from holding too much moisture.
- Once completely cooled, store leftover muffins in an airtight container at room temperature for up to two days. Transfer to the fridge to extend the shelf life.
Notes
- Use spotty bananas: The riper the bananas, the sweeter and more flavorful your muffins will be.
- Mill flour fresh: Grind your wheat berries right before baking to preserve nutrients and the best flavor.
- Don’t over-mix: Once you add the dry ingredients, stir just until combined to keep the muffins light and tender.
- Mix up the chocolate: We like to combine dark and semi-sweet chips for a different taste.
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