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Home » Recipes » Breakfast » Gluten Free Banana Chocolate Chip Muffins

Gluten Free Banana Chocolate Chip Muffins

Modified: Oct 30, 2025 by Molly Pisula · Published: Mar 21, 2022 · As an Amazon affiliate, I earn from qualifying purchases.

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These Banana Muffins with Almond Flour are the perfect afternoon snack. Moist, tender, and packed with banana flavor. Plus, they’re gluten-free! 

plate with banana almond flour muffins stacked in a tower, in front of two bananas

Over the past few years, I’ve developed a number of baking recipes that feature almond flour. The inspiration for this recipe came from one of my favorite banana bread recipes—I decided to try it with almond flour in muffin form and loved the results. My kids have requested these almost daily since I started recipe testing! 

Jump to:
  • Why You'll Love These Gluten Free Banana Bread Muffins
  • What You'll Need to Make Banana Muffins with Almond Flour
  • How to Make Almond Flour Banana Muffins
  • Gluten Free Banana Muffins Recipe Variations and Substitutions
  • How to Store Gluten Free Banana Chocolate Chip Muffins
  • 👩‍🍳 Expert Tips
  • Serving Suggestions for Banana Muffins with Almond Flour
  • FAQs for Gluten Free Banana Almond Flour Muffins
  • Other Almond Flour Baking Recipes
  • 📖 Recipe
  • More About Molly

Why You'll Love These Gluten Free Banana Bread Muffins

  • Great Texture: No dry muffins here! These almond flour banana muffins have the perfect squidgy crumb. 
  • Easy to Make: This recipe does require a mixer, but the ingredients come together quickly. You can make these start to finish in less than 30 minutes! 
  • Healthier than Regular Muffins: Almond flour replaces all-purpose flour in this muffin recipe, giving the muffin protein and fiber. Bananas add fiber and nutrients too! 

What You'll Need to Make Banana Muffins with Almond Flour

chocolate chips, bananas, orange zest, vanilla, baking powder and soda, plain yogurt, almond flour, eggs, and brown sugar
  • Almond Flour: Let’s talk about almond meal vs. almond flour. Really, these are terms both used to mean finely ground almonds. The majority of almond flour products are made by finely grinding blanched almonds (skinless almonds). Almond meal can mean finely ground blanched or unblanched almonds, and almond meal may be a coarser grind than almond flour. For that reason, I generally prefer almond flour in baking. 
  • Yogurt: Any plain (not flavored) yogurt is fine in this recipe. I like the thickness in Greek yogurt, but any style should work. I tested this recipe with a nonfat plain version, but any fat content is ok.
  • Bananas: Extra-ripe bananas are your friend! This is the perfect use for bananas that are too soft to eat. I often buy some extra just so I can let them brown and then make this recipe or this Banana Chocolate Chip Mug Cake!
  • Orange Zest: Feel free to leave this out, or try a slightly different flavor by using lime zest. 
  • Chocolate Chips: These are optional, but I personally love the combination of bananas and chocolate chips! You could try chopped walnuts as an alternative. 

How to Make Almond Flour Banana Muffins

  1. Preheat oven to 350 degrees Fahrenheit. Line a muffin tin with cupcake/muffin liners. Add 2 eggs and ⅔ cup brown sugar to a large mixing bowl, and use a mixer to blend for 2 minutes, until volume doubles in size and mixture lightens.
sugar and eggs whipped in a mixing bowl next to mixer

2. Add ¼ cup plain yogurt and 1 teaspoon vanilla extract, and blend.

wet ingredients in mixing bowl next to mixer and empty bowls with spatula

3. Now, using a wooden spoon, stir in ⅔ cup mashed bananas and 1 teaspoon orange zest.
4. Whisk together 3 ½ cups almond flour, 1 teaspoon baking soda, ½ teaspoon baking power, and ½ teaspoon salt in a smaller bowl, then stir into large bowl with the liquid ingredients. Stir in ½ cup mini chocolate chips (if desired).

almond flour banana muffin batter in mixing bowl with wooden spoon and empty bowls

5. Scoop into the lined muffin tin, filling each cupcake liner close to the top. 

muffin tin filled with batter for almond flour banana muffins

6. Bake for 15-18 minutes, or until a toothpick inserted into the middle of a muffin comes up almost clean. Muffins will be lightly browned.

cupcake tin filled with baked almond flour banana muffins on cooling rack

7. Let cool in muffin tin on rack for 10 minutes, then remove muffins from tin and continue to cool on rack. 

Gluten Free Banana Muffins Recipe Variations and Substitutions

Use this recipe as a base recipe for gluten-free banana muffins. You can remove the chocolate chips, or play around with different types like milk chocolate chips, white chocolate chips, or mini chocolate chips. You can add in toasted chopped nuts, such as walnuts, pecans, or hazelnuts. You might also want to try adding in some toasted shredded coconut.

Try a topping for the muffins as well. Some turbinado or sparkling sugar on top will give you a sweet crunchy top. Or make a streusel topping by combining butter, flour, and brown sugar.

To make these muffins vegan, you will have to replace both the eggs and the yogurt in this almond flour muffin recipe. You could try replacing the eggs with flax eggs, though I haven’t tested that myself. Then replace the yogurt with a non-dairy alternative, like coconut milk yogurt.

How to Store Gluten Free Banana Chocolate Chip Muffins

If you have leftover muffins, leave them out without sealing in an airtight container. If you seal them up, the tops will be sticky the next day. But don't worry, they will easily last a day or two out on a plate, uncovered, as they are plenty moist. See below for freezing instructions.

How to Freeze Almond Flour Banana Muffins

Wait for them to cool completely before putting in a freezer-safe ziploc bag. Store in the freezer for up to 3 months. To defrost, just remove from the freezer and let them sit at room temperature. 

👩‍🍳 Expert Tips

Don’t be afraid to really fill the muffin tin cups. I know most cupcake and muffin recipes will tell you to fill just ⅔ of the way up, but almond flour muffins don’t rise very high so you can add more batter to each cup.

I love to use an ice cream scoop for filling muffin cups. Almost a full scoop is the perfect size to fill these cups! 

Note that these almond flour banana chocolate chip muffins have both soft banana and melted chocolate in them. When you test them with a toothpick after baking, the toothpick may still have banana or melted chocolate on it even when the muffin is done. Test in a couple of spots if you are worried that they aren’t fully cooked. 

Serving Suggestions for Banana Muffins with Almond Flour

These gluten-free banana muffins would be absolutely perfect as part of a breakfast or brunch spread, especially if some of your guests avoid gluten. Check out my Breakfast archive for ideas to pair with these muffins.

Perhaps my Spinach Frittata with Mushrooms and Feta or my Cheesy Crustless Quiche Lorraine? You might also want to try another version of my almond flour muffins, these Almond Flour Blackberry Muffins.

FAQs for Gluten Free Banana Almond Flour Muffins

Can I substitute coconut flour for almond flour?

Unfortunately almond flour and coconut flour really behave differently in baking recipes. Coconut flour will absorb much more liquid than almond flour. In fact, some guides suggest that if you are substituting coconut flour for almond flour, you should use ¼ as much almond flour.

That said, these flours have a similar taste, and coconut flour is lower in calories and fat (though also lower in protein). I would try substituting some of the almond flour with coconut flour and reducing some of the remaining almond flour in the recipe. You could also add moisture by adding more yogurt or another egg if your mixture is too dry. 

Curious about making your own almond flour?

You can do that easily with the help of a food processor. Just take a quantity of blanched almonds (you can often find these as blanched, slivered almonds in the grocery store) and blitz in a food processor until they are finely ground.
Just make sure you stop as soon as you see the texture you want—if you grind for too long, your almond flour will turn into almond butter. 

Why are my almond flour muffins too wet or dense?

Make sure not to overmix the batter, as that can lead to a too-dense texture. And measure the almond flour with a scale if at all possible, because having the wrong almond flour : liquid ratio can affect the texture. Finally, remove the muffins from the tin after they have cooled for a few minutes. Let them finish cooling on a wire rack so that the steam trapped in the muffin tin won’t make the muffins soggy.

How do I prevent my muffins from sinking in the middle?

I highly recommend weighing your ingredients with a scale rather than using measuring cups because the balance of dry and wet ingredients in gluten-free baking is particularly important. Also, do not overmix the batter and make sure that your baking soda and baking power are fresh. Finally, don’t open the oven door in the middle of the bake time.

Are these Banana Almond Flour Muffins healthy?

These banana muffins are under 300 calories each, and are high in protein and fiber. That said, they do contain sugar and sodium. Review the nutrition content in the recipe card below, and you can make the determination yourself whether you think they are healthy.

hands breaking open banana almond flour muffin next to plate with muffins and two bananas

Other Almond Flour Baking Recipes

I love baking with almond flour, and have compiled a round-up of my favorite Almond Flour Dessert Recipes if you're interested in finding more. You might also want to check out my Top Gluten Free Muffin Recipes post. Here are a few more favorites:

  • close-up of chocolate almond flour mug cake with spoon
    Chocolate Almond Flour Mug Cake
  • assortment of 10 almond flour oatmeal cookies on a plate with napkin
    Almond Flour Oatmeal Cookies
  • almond flour chocolate cake on cake stand with slice being removed
    Almond Flour Chocolate Cake
  • close-up of two halves of almond flour zucchini muffin on plate next to strawberries.
    Almond Flour Zucchini Muffins

I also love to combine almond flour and regular flour in my baked goods—regular flour adds structure, and almond flour adds nutrients and that fantastic texture. Here are a few recipes that combine the two:

  • French Yogurt Cake with Almonds
  • Easy Lemon Ricotta Cake
  • Apple Almond Cake

And of course you can find a full assortment of baked goods in my Dessert archive.

If you try this almond flour banana muffin recipe, I would love to hear from you! Leave a comment below—I read them all, and your feedback is invaluable to me.

And please follow along on Instagram, Pinterest, and Facebook or subscribe to my newsletter. I'd love to inspire you with more delicious, healthy, and seasonal recipes!

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stack of banana muffins with almond flour on plate

Gluten Free Banana Bread Muffins

Chef Molly
These Banana Muffins with Almond Flour are the perfect afternoon snack. Moist, tender, and packed with banana flavor.
4.98 from 42 votes
Print Recipe Pin Recipe
Prep Time 10 minutes mins
Cook Time 18 minutes mins
Total Time 28 minutes mins
Course Breakfast
Cuisine American
Servings 12
Calories 290 kcal

Ingredients
  

  • 2 eggs
  • ⅔ cup light brown sugar (138 grams)
  • ¼ cup plain Greek yogurt (61 grams)
  • 1 teaspoon vanilla extract
  • ⅔ cup mashed bananas about 2 bananas (166 grams)
  • 1 teaspoon orange zest
  • 3 ½ cups almond flour (294 grams)
  • 1 teaspoon baking soda
  • ½ teaspoon baking powder
  • ½ teaspoon salt
  • ½ cup mini chocolate chips optional
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Instructions
 

  • Preheat oven to 350 degrees Fahrenheit.
  • Line a muffin tin with cupcake/muffin liners.
  • Add eggs and sugar to a large mixing bowl, and use a mixer to blend for 90 seconds, until volume doubles in size and mixture lightens.
  • Add yogurt and vanilla extract, and blend.
  • Using a wooden spoon, stir in bananas and orange zest.
  • Whisk together almond flour, baking soda, baking power, and salt in a smaller bowl, then stir into large bowl with the liquid ingredients.
  • Stir in chocolate chips (if using).
  • Scoop batter into the lined muffin tin, filling each cupcake liner close to the top.
  • Bake for 15-18 minutes, or until a toothpick inserted into the middle of a muffin comes up almost clean. Muffins will be lightly browned.
  • Let cool in muffin tin on rack for 10 minutes, then remove muffins from tin and continue to cool on rack.

Notes

NOTE: If you have leftover muffins, leave them out on a plate at room temperature rather than sealing in an airtight container. If you seal them up, the tops will be sticky the next day. Don't worry, they are plenty moist so will not be stale the next day. If you want to keep them for longer, freeze them in a ziploc freezer bag, then defrost at room temperture when ready to eat.
Don’t be afraid to really fill the muffin tin cups. I know most cupcake and muffin recipes will tell you to fill just ⅔ of the way up, but almond flour muffins don’t rise very high so you can add more batter to each cup. I love to use an ice cream scoop for filling muffin cups. Almost a full scoop is the perfect size to fill these cups!
Almond Flour Tips: If you are planning to store almond flour for over a few weeks, you should keep it in the refrigerator or freezer. Almond flour (and other nut flours) can turn rancid more quickly than traditional flour. You can make your own almond flour with the help of a food processor. Just take a quantity of blanched almonds (you can often find these as blanched, slivered almonds in the grocery store) and blitz in a food processor until they are finely ground.

Nutrition

Calories: 290kcalCarbohydrates: 25gProtein: 9gFat: 19gSaturated Fat: 3gPolyunsaturated Fat: 16gCholesterol: 31mgSodium: 231mgFiber: 5gSugar: 17g
Tried this recipe?Let us know how it was!

Instagram Users: Now that you've made this recipe, tag me @vanillabeancuisine or #vanillabeancuisine because I'd love to see your results!

More About Molly

Cooking healthy(ish) meals with seasonal ingredients is my passion. Trained as a French pastry chef, I spent over 10 years as a personal chef. Here you'll find well-tested recipes that you and your family will love!

Learn more about me →

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Spicy Mango Dressing »

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Comments

    4.98 from 42 votes (42 ratings without comment)

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  1. Caroline says

    November 05, 2023 at 9:54 pm

    Made this muffins and even baked them 2 minutes past the recommended time …… very disappointing the texture not good as if not cooked properly..

    Reply
    • Molly Pisula says

      November 07, 2023 at 11:37 am

      I'm sorry to hear that, Caroline. Have you baked with almond flour before? The texture is a little different than regular muffins--more moist. Or, I wonder if your bananas were larger than what I usually use? I definitely recommend the cup measurement rather than number of bananas. I make this recipe frequently, and love how it comes out, so if it's not working for someone, I'd love to know why!

      Reply
  2. Sara says

    March 21, 2022 at 11:38 am

    These look great! I have some frozen bananas that I’ve been saving for recipes. I think I’ve found my next breakfast recipe to try!

    Reply
    • Chef Molly says

      March 21, 2022 at 3:08 pm

      Yes! I love freezing bananas for uses like this. Enjoy!

      Reply

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I'm Molly, a former personal chef trained in French pastry. Here you'll find veggie-forward, seasonal recipes with a little French kiss!

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