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Cream Cheese-Filled Almond Flour Banana Muffins (Gluten-Free)

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If you love banana bread, you love these grain free Cream Cheese-Filled Almond Flour Banana Muffins for a delicious gluten-free breakfast.

Cream Cheese-Filled Almond Flour Banana Muffins
Cream Cheese-Filled Almond Flour Banana Muffins

If your house is anything like mine, our bananas seem to get ripe faster than we can eat them. But that’s never a problem because my family loves when I bake banana bread or muffins, so the riper, the better! When I made these Almond Flour Banana Cream Cheese Muffins for my family, they couldn’t get enough. Some other healthy banana muffin recipes to try are these Maple Pecan Banana Muffins and Chocolate Chocolate Chip Banana Muffins.

Cream Cheese-Filled Banana Muffins

These banana cream cheese muffins are loaded with ripe bananas and stuffed with cream cheese and sugar. They come out so incredibly moist they almost fall apart. These muffins are also gluten-free, as I used almond and coconut flours instead of wheat.

Almond flour which is made from ground almonds is incredibly nutritious. Especially rich in vitamin E and magnesium, two important nutrients for health according to Healthline.

What is the secret to making moist muffins?

I have a few secrets for making moist banana muffins.

  • Almond flour has more fat than wheat which makes these muffins moister than wheat flour.
  • The cream cheese in the middle adds a lot of creaminess.
  • Ripe bananas give these muffins moisture while also reducing the fat and sugar needed.

How to Store, Freeze, and Reheat Banana Muffins

Muffins are great for meal prep. One batch makes 12 cream cheese-filled muffins, which will last in the fridge for four to five days. You can also freeze muffins by individually wrapping them in plastic wrap or foil and storing them in a zip-locked bag or container.

You can pull the muffins out of the freezer as you need them. Just place in the refrigerator overnight and warm in the microwave for about 20 seconds. You can also microwave them straight from the freezer for a little longer.


  • Top with chopped almonds, pecans or walnuts or mix in half a cup of nuts for banana nut muffins.

Cream Cheese Allmond Flour Banana MuffinsCream Cheese-Filled Banana Muffins

More Healthy Muffin Recipes You’ll Love:

Cream Cheese-Filled Almond Flour Banana Muffins (GF)

5 from 33 votes
If you love banana bread, you love these grain free Cream Cheese-Filled Almond Flour Banana Muffins for a delicious gluten-free breakfast.
Course: Breakfast, Dessert
Cuisine: American
Cream Cheese-Filled Banana Muffins
Prep: 20 minutes
Cook: 40 minutes
Total: 1 hour
Yield: 12 servings
Serving Size: 1 muffin


  • 1 2/3 cups very ripe bananas, from 3 medium
  • 1 cup almond flour
  • 1/3 cup coconut flour
  • 2 teaspoons baking powder
  • 1/2 teaspoon baking soda
  • 1/4 teaspoon salt
  • 2 tbsp butter, softened
  • 1/3 cup unpacked brown sugar, divided
  • 2 large eggs
  • 1 tsp vanilla extract
  • 4 ounces reduced fat cream cheese


  • Preheat oven to 325°F. Line cupcake tin with liners.
  • Mash bananas in a bowl, set aside.
  • In a medium bowl, combine almond flour, coconut flour, baking powder, baking soda and salt with a wire whisk. Set aside.
  • In a large bowl cream butter and 1/4 cup of the sugar with an electric mixer.
  • Add eggs, bananas and vanilla; beat at medium speed until thick. Scrape down sides of the bowl.
    batter for almond flour banana muffins
  • Add flour mixture, then blend at low speed until just combined.
  • Mix the cream cheese and remaining sugar.
  • Pour half the batter into muffin pan then add about 2 teaspoons of cream cheese to the center of each muffin and top with the remaining batter; bake on the center rack for 35 to 45 minutes, or until a toothpick inserted in the center comes out clean.
    Almond Flour Banana Cream Cheese Muffins

Last Step:

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Serving: 1 muffin, Calories: 149 kcal, Carbohydrates: 13.5 g, Protein: 5 g, Fat: 8.5 g, Saturated Fat: 2.5 g, Cholesterol: 42 mg, Sodium: 209.5 mg, Fiber: 3 g, Sugar: 8.5 g


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104 comments on “Cream Cheese-Filled Almond Flour Banana Muffins (Gluten-Free)”

  1. Excellent! Very tasty muffins that make a great breakfast or afternoon snack. Great flavor for being gluten free and very moist. Kids loved them!

  2. A very indulgent recipe. I used 3 eggs ( eggs seem to be looking smaller) and the cupcakes were the best ever( 1/2 tsp cinnamon also).
    Would pumpkin work instead of banana? Trying to find healthy ways to use my almond flour.

    1. It didn’t come out as good when I tested it with just almond flour, it doesn;t hold together as well. But you can.

  3. I can’t begin to say how delicious this recipe is. I’ve been trying to eat more healthy without completely making my diet bland. This did the trick and then some. I’m looking forward to trying more recipes.

  4. Amazing!! Better than I thought given how healthy they are! Definitely a keeper. Any idea if this can be baked in a loaf pan instead of cupcakes, and if so, what temp and time?

  5. I made this recipe and shared with my co-workers. They all loved it! These muffins are so easy, moist, and delicious. Thank you, Gina!

  6. This is the first gluten free item I have made. Shocking how good these are. I just didn’t expect it. Yum!

  7. I wonder if you can substitute brown sugar for brown coconut sugar? And how much? To me, coconut sugar isn’t as sweet.

  8. Can you please be more specific in item 4?  How much cream cheese was supposed to be mixed in with the butter and sugar?

    1. Im not the author but it doesn’t say to mix in with butter. It says to use 1/4 of the brown sugar (of the 1/3)with the butter mixture. Then in a separate bowl mix the rest of the brown sugar ( which should not be much) with the cream cheese ( half of the box). That will go on top of the batter then you cover the cream cheese with more batter. I haven’t tried this recipe but will today.

  9. Hi! We love your recipes!!  The maple banana pecan muffins are a staple in our house!  For this recipe, can I use additional almond flour for the 1/3 cup coconut flour?

  10. These were insanely good and you would never know they were GF. My 9 year old daughter helped me make them and we absolutely loved them. I try to avoid sugar so I subbed brown sugar swerve for the brown sugar.  Soooo good. Will 1000% make again. 

  11. These were an absolute hit in my house. The only advice before making these: double the recipe!! My husband ate 5 on the first day, and by day two, these amazing muffins were gone. So sad. I’m definitely making them again!

  12. Do you have a recipe that doesn’t use almond flour? Or can I substitute regular flour? I’m allergic to tree nuts, but these look amazing! 

  13. My son loves these – he just got braces and we are always looking for soft but not sugar-heavy processed foods. Making another batch now for the week!

  14. Avatar photo
    Peggy Rouleau

    These are outstanding. I got the WW PP down to 4 just by reducing brown sugar to 1T. The bananas make them plenty sweet for me. Great low point snack with afternoon tea.

  15. Delicious, moist, flavorful. I subbed AP Flour instead of coconut flour, and I only had 1 and 1/3 cups banana after mashing so I added 1/3 cup unsweetened applesauce.
    I added 1/2 tsp cinnamon and a pinch of nutmeg and a little maple syrup to cream cheese.
    Had great taste, a real treat

  16. Made these for breakfast this morning. Pretty good! I used coconut sugar instead of brown sugar and regular cream cheese instead of reduced fat. I was debating adding cinnamon to the batter and decided not to, but next time I’d add it to either the batter or cream cheese. They came out moist and delicious, not too sweet. 

  17. So I made these finally
    Only sub was Quark for cream cheese.
    They came out overly moist, maybe I’ll try 3 banana Vs measuring 1 and 2/3 cup mashed banana as that used 4.  Not sure what else I could have done wrong.

  18. I am trying to avoid added sugar. What would you suggest to replace the brown sugar? I was thinking maple syrup or dates.

  19. So I have a macros calculation question.
    I’ve keyed all my ingredients into MFP.
    4 of the ingredients have fat (I used quark as sub for cream cheese so no fat)
    2T Natrel unsalted butter 24g
    2 large eggs 10g
    16T Kirkland almond flour 128g
    1/3 C coconut flour. 5g
    That gives me 14g of fat per muffin vs 8.5g in the recipe.
    Where did I go wrong?

    btw – love love love your recipes!!!

    1. I think your 12 T of almond flour for 128g of fat is off. I just measured 12 T almond flour – it weighs 2.8 oz. 1 oz of almond flour has 14g of fat, so 2.4 would give you around 30g of fat.

  20. Question, I want to try this but was wondering if those are mini muffin tins or regular size? I think it will make difference with cooking time if I use the larger ones.


  21. Hi Gina, A lovely yummy muffin. These worked great with whipped cream cheese. I also added 1/4 tsp cinnamon to the batter. Next time, I am going to add a little vanilla or maple extract to the cream cheese mixture.
    I appreciate the cup measurements on the bananas.

    I have made your fudgy cookie recipe with almond flour ( excellent) . I hope you try some other creations with almond flour. Maybe something with chicken etc.

  22. HI Gina, Can whipped lite cream cheese be used or does it need to be in block form? Whipped sometimes works great in some recipes ( your banana cream pie) but not always with baking
    I cannot wait to try your newest muffin recipe. My family love all your muffin recipes that can be made gluten free.
    Stay well and warm,

    I hope this works…
    I am allergic to coconut, so I searched for substitutes for coconut flour and found this conversion chart.  Haven’t tried it yet, but I certainly will

  24. Avatar photo
    Daphne Clifford

    Just made these this morning!!! Wow what a tender, decadent, fun filled creamy absolutely delicious muffin that I’ve ever taste😊 Gotta make these people!!!

  25. So I think everyone wants to know what to do without coconut flour haha. I also, didn’t have coconut flour, but I love almond flour for the flavor, texture, and protein. So I replaced the coconut flour with just AP flour and it worked great. They were a bit denser and chewier than probably most muffins, but my family devoured them nonetheless. If you are wondering about this substitution, go for it.  

  26. Loved this! I made it with King Arthur’s measure for Measure gluten free flour and it was amazing! My GF friends are eternally grateful 🙂
    You can also ripen (peels on) bananas in the oven at 350 for 30 min- check at 15.
    Any idea how this would shake out for WW Points?
    Thank you. Love Skinnytaste!

  27. Absolutely fantastic 😋This recipe will be a keeper for me and I am not gluten free.The ingredients called to me and I am so happy I answered the call!

  28. These are delicious! My daughter and I made them the other night, and she didn’t even fuss knowing that we didn’t use traditional flour. The cream cheese made me feel like I was eating something decadent, and we even put a few chocolate chips in some for a tasty, sweet surprise!

    1. I used oat flour instead of the coconut flour. They turned out great! They’re probably tastier with coconut flour though!

      1. thanks for tip, I have almond flour but don’t want a bunch of different types of flour around to wonder how to use up” will try this.

  29. I don’t have coconut flour, can I use almond flour only? And can I replace the butter for apple sauce? Thanks! 🙂

  30. Looks great and my stepdaughter is gluten free. Can all almond be used or is there a sub for the coconut?

  31. These look delicious and I love all of your recipes that I’ve tried! I can usually save recipes from the site to Relish, but don’t see an option here that will do that. Can you make this savable? Thanks in advance! Can’t wait to try these. 

  32. My husband is not a cream cheese lover so wondered is it necessary for moisture or can I just leave it out?

    1. No, use this recipe instead as a base…

  33. These sound amazing and I’d love to make them for husband when he gets out of the hospital. I don’t keep almond or coconut flour, would I just use the same amount of whole wheat or AP?  Thanks so much for your help!  We love all your recipes!

    1. No, you can use this recipe instead as a base…

  34. I was wondering if I could use regular flour as I don’t keep the others around and I don’t care about gluten-free. Thanks!

    1. No but you can use this recipe as a base instead…

  35. How did you know I’ve been planning on making banana bread hehe 🙂 I don’t usually keep coconut flour around, so I was wondering if using almond flour only would work?

  36. As good as they look. So flavorful…I ate 2, I couldn’t help it. I didn’t hVe cocoanut flour so just processed some unsweetened cocoanut in food processor until fine. Perfect. Thanks gina

    1. Thanks so much for this idea.  I don’t have coconut flour on hand, but have plenty to unsweetened coconut and a food processor. You just saved me a trip to the store and saved me from buying a bag of coconut flour when I only need 1/3 cup.  

  37. Excited to make these but don’t have coconut flour on hand. Can I sub 1:1 with more almond flour?