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Home » Fall Recipes

Whole Wheat Banana Muffins with Chocolate Chips

Published: May 12, 2026 by Stephanie · This post may contain affiliate links · Leave a Comment

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Whole wheat banana muffins are one of my favorite ways to use up ripe bananas when I want something simple, homemade, and easy to serve for breakfast or snacks. These muffins are soft, moist, and made with fresh milled soft wheat flour, brown sugar, and chocolate chips for just the right amount of sweetness. If you enjoy baking with fresh milled flour, you may also like my Whole Wheat Pancakes Recipe with Fresh Milled Flour and Sourdough Option.

Fresh baked whole wheat banana muffins with chocolate chips served warm in a muffin pan.

I love this recipe because it feels practical and cozy at the same time. It uses everyday ingredients, comes together quickly, and makes a full muffin pan of banana muffins that are perfect warm from the oven or saved for later in the week. For another sweet fresh milled recipe, my Chocolate Milled Wheat Sourdough Quick Bread Recipe is a good one to try next.

Table of Contents

  • What Are Whole Wheat Banana Muffins?
  • Quick Look at This Recipe
  • Why You’ll Love These Whole Wheat Banana Muffins
  • How to Store Whole Wheat Banana Muffins
  • What to Serve with Whole Wheat Banana Muffins
  • Ingredients
  • Equipment
  • How to Make Sourdough Discard Banana Muffins with Chocolate Chips
  • Tips for the Best Whole Wheat Banana Muffins
  • Frequently Asked Questions About Whole Wheat Banana Muffins
    • Can I use all-purpose flour instead of whole wheat flour?
    • Can I use store-bought whole wheat flour?
    • What kind of wheat berries should I use for banana muffins?
    • Can I make these banana muffins without chocolate chips?
    • Why did my banana muffins sink in the middle?
    • Tried this recipe?

This post contains affiliate links, which means I make a small commission at no extra cost to you. See my full disclosure here.

Close-up of a whole wheat banana muffin with melted chocolate chips and a moist crumb.

What Are Whole Wheat Banana Muffins?

Whole wheat banana muffins are soft, moist banana muffins made with ripe bananas, whole wheat flour, brown sugar, eggs, milk, butter, baking soda, baking powder, and chocolate chips. This recipe uses fresh milled soft wheat flour, which gives the muffins a hearty homemade flavor while still keeping the texture tender. These muffins are a simple way to bake with whole grain flour without making the recipe feel heavy or dry.

Quick Look at This Recipe

Prep time: 10 minutes
Bake time: 18 to 24 minutes
Total time: 30 to 35 minutes
Servings: 12 muffins
Texture: Soft, moist, tender, and lightly hearty
Best served: Warm with butter, coffee, milk, or as an easy breakfast or snack

Homemade whole wheat banana muffins with chocolate chips on a plate beside a muffin pan.

Why You’ll Love These Whole Wheat Banana Muffins

These whole wheat banana muffins are easy to make and do not require sourdough starter or sourdough discard. They are a true banana muffin recipe made with ripe bananas, fresh milled flour, brown sugar, and chocolate chips.

The bananas keep the muffins moist, the brown sugar gives them a warm sweetness, and the soft wheat flour adds that fresh milled flavor I love. If you are trying to use more freshly milled flour in everyday baking, these muffins are a good place to start.

If you enjoy baking breakfast recipes with fresh milled flour, you may also like my Whole Wheat Donuts Made with Fresh Milled Flour.

How to Store Whole Wheat Banana Muffins

Store cooled muffins in an airtight container at room temperature for 2 to 3 days.

For longer storage, keep them in the refrigerator for up to 5 days. You can also freeze them for up to 3 months. Let the muffins cool completely, then place them in a freezer-safe bag or container.

To serve, thaw at room temperature or warm gently before eating.

Fresh whole wheat banana muffins with chocolate chips showing a soft, moist center.

What to Serve with Whole Wheat Banana Muffins

These muffins are delicious warm with butter, a cup of coffee, or a glass of milk. They also make a simple breakfast with deviled eggs, homemade yogurt, or fresh fruit.

For another homemade snack made with milled wheat, try my Homemade Milled Wheat Sourdough Graham Crackers. If you love chocolate then my Chocolate Milled Wheat Sourdough Quick Bread Recipe is another satisfying recipe to make with fresh milled flour.

Ingredients for whole wheat banana muffins with chocolate chips, including fresh milled flour, ripe bananas, eggs, brown sugar, milk, butter, and chocolate chips.

Ingredients

3 very ripe bananas, mashed
½ cup butter, melted and slightly cooled
â…” cup brown sugar
2 large eggs
1 teaspoon vanilla extract
¼ cup milk
2 cups soft milled wheat flour, 286 g
1 teaspoon baking soda
½ teaspoon baking powder
½ teaspoon salt
1 teaspoon cinnamon, optional
1 cup chocolate chips, plus extra for topping

Equipment

Large mixing bowl
Medium mixing bowl
Fork or potato masher
Whisk
Spatula
Measuring cups and spoons
Muffin pan or muffin tin
Paper muffin cups or butter for greasing
Cooling rack

How to Make Sourdough Discard Banana Muffins with Chocolate Chips

Mashed ripe bananas in a glass mixing bowl for whole wheat banana muffins with chocolate chips.

Step 1: Preheat the oven to 350°F. Line a 12-cup muffin tin with paper liners or grease each muffin cup well. In a large mixing bowl, mash the very ripe bananas until mostly smooth. A few small banana pieces are fine and will give the muffins good texture.

Mashed bananas, brown sugar, eggs, milk, vanilla, and melted butter in a glass bowl for whole wheat banana muffins.

Step 2: Add the melted butter, brown sugar, eggs, vanilla extract, and milk to the mashed bananas. Stir until the wet ingredients are well combined.

Fresh milled wheat flour, baking soda, baking powder, salt, and cinnamon in a glass mixing bowl.

Step 3: In a separate bowl, whisk together the soft milled wheat flour, baking soda, baking powder, salt, and cinnamon if using.

Whole wheat banana muffin batter being gently mixed with a spatula.

Step 4: Add the dry ingredients to the banana mixture and stir gently until just combined. Do not overmix the batter, or the muffins can turn out dense.

Chocolate chips added to whole wheat banana muffin batter in a glass bowl.

Step 5: Fold in the chocolate chips.

Whole wheat banana muffin batter divided into paper liners in a muffin tin before baking.

Step 6: Spoon the batter evenly into the prepared muffin tin, filling each cup about ¾ full. Sprinkle a few extra chocolate chips on top if desired.

Baked whole wheat banana muffins with chocolate chips cooling in a black muffin pan.

Step 7: Bake for 18 to 24 minutes, or until the tops are set and a toothpick inserted into the center of a muffin comes out clean or with a few moist crumbs. Let the muffins cool in the pan for about 5 minutes, then move them to a cooling rack.

Tips for the Best Whole Wheat Banana Muffins

Use very ripe bananas for the best flavor and moisture.

Do not pack the flour tightly into the measuring cup. If using fresh milled flour, weigh 286 g for the most accurate result.

Stir the dry ingredients into the wet ingredients gently. Overmixing can make muffins dense.

Let the batter sit for 5 minutes before baking if your fresh milled flour seems very thirsty.

Fill the muffin cups about ¾ full so the muffins have room to rise.

Add a few extra chocolate chips on top before baking for a prettier muffin.

Fresh whole wheat banana chocolate chip muffin broken open to show the tender, moist crumb and melted chocolate inside.

Frequently Asked Questions About Whole Wheat Banana Muffins

Can I use all-purpose flour instead of whole wheat flour?

Yes, you can use all-purpose flour instead of whole wheat flour in this banana muffin recipe. The muffins may be a little lighter and less hearty, but the recipe will still work. Start with the same amount of flour and watch the batter texture. It should be thick but scoopable, not runny.

Can I use store-bought whole wheat flour?

Yes, you can use store-bought whole wheat flour instead of fresh milled soft wheat flour. The muffins may be slightly denser, but they will still be soft and flavorful. If the batter seems too thick, add a small splash of milk before scooping it into the muffin pan.

What kind of wheat berries should I use for banana muffins?

Soft wheat berries work best for whole wheat banana muffins because they make a lighter, more tender flour. Hard wheat can be used, but it may make the muffins heavier and more dense.

Can I make these banana muffins without chocolate chips?

Yes, you can leave out the chocolate chips for a more classic banana muffin. You can also replace them with chopped walnuts or pecans if you want to make whole wheat banana nut muffins.

Why did my banana muffins sink in the middle?

Banana muffins can sink if they are underbaked, overmixed, or if the muffin cups are filled too high. Bake until the centers are set and a toothpick inserted into the middle comes out clean or with a few moist crumbs.

Tried this recipe?

I would love to see it! Tag me on Instagram @idiesfarm and #idiesfarm so I can share your beautiful creation!

Whole wheat banana chocolate chip muffin broken open to show melted chocolate and a soft, moist center.

Whole Wheat Banana Muffins with Chocolate Chips

Soft and moist whole wheat banana muffins made with fresh milled soft wheat flour, ripe bananas, brown sugar, and chocolate chips. These easy homemade muffins are tender, lightly hearty, and perfect for breakfast, snacks, or using up ripe bananas.
Print Pin Rate
Prep Time: 10 minutes minutes
Cook Time: 18 minutes minutes
Total Time: 35 minutes minutes
Servings: 12 muffins
Author: Stephanie

Equipment

  • Large mixing bowl
  • Medium mixing bowl
  • Fork or potato masher
  • Whisk
  • spatula
  • Measuring cups and spoons
  • Muffin pan or muffin tin
  • Paper muffin cups or butter for greasing
  • cooling rack

Ingredients

  • 3 very ripe bananas mashed
  • ½ cup butter melted and slightly cooled
  • â…” cup brown sugar
  • 2 large eggs
  • 1 teaspoon vanilla extract
  • ¼ cup milk
  • 2 cups soft milled wheat flour 286 g
  • 1 teaspoon baking soda
  • ½ teaspoon baking powder
  • ½ teaspoon salt
  • 1 teaspoon cinnamon optional
  • 1 cup chocolate chips plus extra for topping if desired

Instructions

  • Preheat the oven to 350°F. Line a 12-cup muffin tin with paper liners or grease each muffin cup well. In a large mixing bowl, mash the very ripe bananas until mostly smooth. A few small banana pieces are fine and will give the muffins good texture.
  • Add the melted butter, brown sugar, eggs, vanilla extract, and milk to the mashed bananas. Stir until the wet ingredients are well combined.
  • In a separate bowl, whisk together the soft milled wheat flour, baking soda, baking powder, salt, and cinnamon if using.
  • Add the dry ingredients to the banana mixture and stir gently until just combined. Do not overmix the batter, or the muffins can turn out dense.
  • Fold in the chocolate chips.
  • Spoon the batter evenly into the prepared muffin tin, filling each cup about ¾ full. Sprinkle a few extra chocolate chips on top if desired.
  • Bake for 18 to 24 minutes, or until the tops are set and a toothpick inserted into the center of a muffin comes out clean or with a few moist crumbs. Let the muffins cool in the pan for about 5 minutes, then move them to a cooling rack.

Notes

Tips for the Best Whole Wheat Banana Muffins

Use very ripe bananas for the best flavor and moisture.
Do not pack the flour tightly into the measuring cup. If using fresh milled flour, weigh 286 g for the most accurate result.
Stir the dry ingredients into the wet ingredients gently. Overmixing can make muffins dense.
Let the batter sit for 5 minutes before baking if your fresh milled flour seems very thirsty.
Fill the muffin cups about ¾ full so the muffins have room to rise.
Add a few extra chocolate chips on top before baking for a prettier muffin.
About Idies at Idiesfarm.com.

Welcome!

Hi! I’m Stephanie, also known as Idie. Follow me as I tap into the methods of the past and learn how to make my world a little smaller.

More about me

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