Got a bunch of brown bananas on the counter and leftover cottage cheese in the fridge sitting on the counter staring you down? Don’t toss them! Instead, you should use both to make these incredible gluten free and refined sugar free Cottage Cheese Banana Muffins! This protein-packed muffin recipe is completely gluten-free, comes together in a flash, and yields the fluffiest, moistest crumb thanks to a secret blended ingredient.

What makes these gluten free cottage cheese muffins a great option for busy mornings is how effortlessly they deliver real nutrition and taste. Whipping the cottage cheese until completely smooth adds high-quality protein without changing the classic banana bread flavor you love (especially with the chocolate and nuts). Balanced with almond flour, cassava flour, and a touch of warm cinnamon, they stay moist for days without drying out.
If you love simple, protein-packed bakes, you will want to save a few more kitchen favorites to your weekly rotation. Try these Easy Overnight High Protein French Toast Casserole or these Gluten Free Blueberry Oatmeal Protein Pancakes for more meal-prep, quick morning meals, or bake a loaf of Protein Banana Nut Bread with Protein Cream Cheese Frostin) to use up extra bananas. For more cottage cheese meal-prep options, these cottage cheese recipes would be a great place to look!
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Why You’ll Love This Banana Muffin Recipe
- It's packed with protein. Made with whipped cottage cheese, eggs, almond flour, and protein powder, it's a great option for anyone trying to increase their protein intake without giving up a sweet treat.
- It is a perfect breakfast & snack. Delicious, protein-packed, and easy to bake, making these muffins the perfect breakfast and/or snack.
- Ideal for weekly meal prep. A single batch of these muffins bakes so quickly on a Sunday, providing nutritious grab-and-go options for busy mornings or when you are needing a snack.
- Naturally gluten free & grain free. Almond flour and cassava flour offer a wholesome alternative for anyone managing gluten sensitivities or allergies.

Banana Cottage Cheese Muffin Ingredients (and Substitutions)
- Ripe Fresh Bananas. The riper the better for the sweetest, most banana-forward flavor.
- Whipped Cottage Cheese. The secret weapon for adding moisture and extra protein without drying out the crumb of the quick bread. Simply swap the cottage cheese in the banana bread batter for a thick dairy-free yogurt for a dairy-free bread result.
- Eggs.
- Vanilla. Classic add-in for baked goods.
- Coconut Sugar. This recipe skips refined white sugar entirely by using coconut sugar, which adds a wonderful caramel-like depth that pairs perfectly with the spices.
- Avocado Oil. A light, neutral oil that keeps the crumb perfectly moist (especially with gluten-free flours). I do not recommend using extra-virgin olive oil as it will add a strong flavor to the cake that you don't want.
- Almond Flour & Cassava Flour. The almond flour provides moisture, while the cassava gives it that classic cake structure you know and love.
- Vanilla or Banana Protein Powder. Adds sweetness and a major protein boost. Banana protein powder would work beautifully here to boost that banana bread flavor, too! My favorite brand of protein powder to use is Equip Foods. Use the code PRETTYDELISH for a discount.
- Baking Soda & Baking Powder. These are leavening agents to help the muffins rise properly.
- Salt.
- Cinnamon. A perfect addition to any banana bread recipe! This high protein breakfast or snack recipe has it all.
- Nuts & Chocolate Chips. These are the best add-ins to include inside the banana muffins for flavor and texture.

Gluten Free Banana Muffin Step by Step Instructions
1. Prep. Preheat oven to 350 F. Line a muffin tin with parchment muffin liners and set aside until the batter is ready.
2. Peel and Mash Banana. Peel three very ripe bananas and add them to a large mixing bowl. Mash thoroughly with a fork until no large chunks remain and the bananas are mostly smooth. Set aside.


3. Whip Cottage Cheese. Put the cottage cheese in the food processor and blend until smooth and fluffy, about 1-2 minutes. Leave in the food processor until you are ready for it.

4. Mix Wet Ingredients. Add the eggs, vanilla, whipped cottage cheese, and coconut sugar to the bowl with the mashed bananas and whisk until fully incorporated. Whisk in the avocado oil until everything is combined.


5. Add Dry Ingredients. Add the almond flour, cassava flour, protein powder (vanilla or banana), baking soda, baking powder, salt and cinnamon to the same mixing bowl and fold together using a silicone spatula until fully combined. Make sure there are no clumps or flour or protein powder.



6. Fold in Nuts and Chocolate Chips. Fold in the chopped nuts and chocolate chips until evenly distributed throughout the batter.


7. Pour Batter in Muffin Tin. Using a ¼ cup measuring cup, scoop the batter into the muffin tin until each cup is just about full. Don’t worry, since this is gluten free it won’t spill over when baking!



8. Bake. Bake the banana muffins for 20 to 25 minutes until a toothpick comes out clean when poked in the center of the muffin.
Cottage Cheese Muffins Expert Tips & Tricks
- Don't over-mix the batter. Once the dry ingredients go into the wet ingredients, fold gently with a silicone spatula just until combined. Over-mixing leads to a tougher crumb.
- Whip the cottage cheese thoroughly. Run your food processor until no visible curds remain. A smooth consistency blends seamlessly into the wet ingredients.
- Use ripe brown bananas: Bananas with heavy brown spots are naturally sweet and add a lot of moisture, reducing the need for refined sugars.
- Fill the muffin cups fully: Because this batter does not spill over drastically, scoop it until each cup is almost completely filled for full-sized muffins.
- Toast the nuts before folding into the batter: Giving your pecans or walnuts a brief five-minute toast in a dry skillet or in the oven deepens their nutty flavor inside the batter and takes the gluten free banana muffin batter to a whole new level.

Cottage Cheese Muffin Frequently Asked Questions
Are these Banana Cottage Cheese Muffins gluten-free?
Yes, this banana muffin recipe relies on a combination of almond flour and cassava flour, making it completely grain-free and naturally gluten-free. So if you cannot have gluten but still want a tasty to-go snack or easy breakfast, these muffins are a great option.
Do I need a food processor to blend the cottage cheese?
A food processor, high-speed blender, or immersion blender will all work effectively to remove the curds and whip the cottage cheese smooth.
Why did my gluten free muffins not rise high over the top of the tin?
Gluten-free flours like almond and cassava are denser than traditional wheat flour, so they expand less while baking. Filling each muffin tin almost full ensures a nice, rounded muffin top.
Can I make this recipe without the protein powder?
The protein powder is completely optional, but it does add more protein without changing the texture of the muffin too much. If you skip it, the batter remains well-balanced and bakes up wonderfully.
Can I leave out the chocolate chips or nuts?
Absolutely. If you aren't a fan of chocolate chips in your banana bread or have a nut allergy, you don't have to include them. These ingredients add more flavor and crunch to the soft, moist banana bread recipe.
Can I use a different sweetener instead of coconut sugar?
If you want to keep this easy banana muffin recipe entirely free from added refined sugars, you can swap the coconut sugar for an equal amount of granulated monkfruit. It bakes similarly and still gives you great results without the blood sugar spike. I wouldn't recommend liquid sweeteners like maple syrup, as it will change the ratio of wet to dry ingredients in the batter.

How to store these banana cottage cheese muffins
Store these muffins in an airtight container or ziplock bag with air removed, in the refrigerator for about 3-5 days. Because of the cottage cheese, I recommend keeping them refrigerated rather than leaving them out at room temperature after the first day.
To freeze let the muffins cool completely, then wrap the individual cooled muffins in plastic wrap or store them together in a freezer-safe bag for up to 3 months. Thaw the muffins at room temperature or warm briefly in the microwave for 30 to 60 seconds.
If you liked this recipe, you might also enjoy these...
- Gluten Free Blueberry Cottage Cheese Protein Muffins
- Gluten Free Pumpkin Muffins
- Gluten Free Blueberry Protein Muffins
- Protein Banana Nut Bread with Protein Cream Cheese Frosting (Easy & Gluten Free)
- Chocolate Chip Banana Protein Cookies (Gluten Free)
- 20+ Easy to Make High Protein Cottage Cheese Recipes
Did you have a chance to make this recipe? If so, please leave me a 5 star rating and review below. I always love and appreciate hearing from you!

Protein Banana Cottage Cheese Muffins
Equipment
- 1 Muffin Tin
- 1 Food Processor
- Measuring Cups + Spoons
Ingredients
- 3 very ripe bananas, mashed about 1 to ¼ cups
- ½ cup cottage cheese whipped smooth
- 2 large eggs
- 1 tablespoon vanilla
- 3 tablespoons coconut sugar
- ¼ cup avocado oil or neutral oil of choice
- 1 ½ cups almond flour
- ½ cup cassava flour
- 1 scoop (about ¼ cup) banana protein powder or vanilla protein powder (optional)
- 1 teaspoon baking soda
- 1 teaspoon baking powder
- ½ teaspoon salt
- 2 teaspoons cinnamon
- ⅓ cup chopped nuts of choice , I recommend pecans or walnuts
- ¼ cup chocolate chips
Instructions
- Prep. Preheat oven to 350 F. Line a muffin tin with parchment muffin liners and set aside until the batter is ready.
- Peel & Mash Banana. Peel three very ripe bananas and add them to a large mixing bowl. Mash thoroughly with a fork until no large chunks remain and the bananas are mostly smooth. Set aside.
- Whip Cottage Cheese. Put the cottage cheese in the food processor and blend until smooth and fluffy, about 1-2 minutes. Leave in the food processor until you are ready for it.
- Mix Wet Ingredients. Add the eggs, vanilla, whipped cottage cheese, and coconut sugar to the bowl with the mashed bananas and whisk until fully incorporated. Whisk in the avocado oil until everything is combined.
- Add Dry Ingredients. Add the almond flour, cassava flour, protein powder, baking soda, baking powder, salt and cinnamon to the same mixing bowl and fold together using a silicone spatula until fully combined. Make sure there are no clumps or flour or protein powder.
- Fold in Nuts & Chocolate Chips. Fold in the chopped nuts and chocolate chips until evenly distributed throughout the batter.
- Pour Batter in Muffin Tin. Using a ¼ cup measuring cup, scoop the batter into the muffin tin until each cup is just about full. Don’t worry, since this is gluten free it won’t spill over when baking!
- Bake. Bake for 20 to 25 minutes until a toothpick comes out clean when poked in the center of the muffin.
Notes
- Don't over-mix the batter. Once the dry ingredients go into the wet ingredients, fold gently with a silicone spatula just until combined. Over-mixing leads to a tougher crumb.
- Whip the cottage cheese thoroughly. Run your food processor until no visible curds remain. A smooth consistency blends seamlessly into the wet ingredients.
- Use brown bananas: Bananas with heavy brown spots are naturally sweet and add a lot of moisture, reducing the need for refined sugars.
- Fill the muffin cups fully: Because this batter does not spill over drastically, scoop it until each cup is almost completely filled for full-sized muffins.
- Toast the nuts before folding into the batter: Giving your pecans or walnuts a brief five-minute toast in a dry skillet or in the oven deepens their nutty flavor inside the batter and takes the gluten free banana muffin batter to a whole new level.
- How to store these banana cottage cheese muffins. Store these muffins in an airtight container or ziplock bag with air removed, in the refrigerator for about 3-5 days. Because of the cottage cheese, I recommend keeping them refrigerated rather than leaving them out at room temperature after the first day. To freeze let the muffins cool completely, then wrap the individual cooled muffins in plastic wrap or store them together in a freezer-safe bag for up to 3 months. Thaw the muffins at room temperature or warm briefly in the microwave for 30 to 60 seconds.





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