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 Banana Muffins
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5 from 18 votes
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Cream Cheese-Filled Banana Muffins

149 Cals 5 Protein 13.5 Carbs 8.5 Fats
Prep Time: 20 mins
Cook Time: 40 mins
Total Time: 1 hr
Yield: 12 servings
COURSE: Breakfast, Dessert
CUISINE: American
If you love banana bread, you love these grain free Cream Cheese-Filled Almond Flour Banana Muffins for a delicious gluten-free breakfast.


  • 1 2/3 cups from 3 medium very ripe bananas
  • 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


Serving: 1muffin, Calories: 149kcal, Carbohydrates: 13.5g, Protein: 5g, Fat: 8.5g, Saturated Fat: 2.5g, Cholesterol: 42mg, Sodium: 209.5mg, Fiber: 3g, Sugar: 8.5g
Keywords: almond flour muffins, banana bread muffins, gluten free banana bread

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  1. 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!

  2. Good luck eating only 1!

  3. 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.

  4. 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

  5. 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. 

  6. 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.

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

  8. 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!!!

    • 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.

  9. Question. Can these be frozen after? If not how should they be stored and for how long?

  10. 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.


  11. 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.

  12. 10 out of 10 – easy to make and delicious

  13. 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

  15. 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!!!

  16. 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.  

  17. 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!

  18. Will the muffins turn out the same using full fat cream cheese?

  19. 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!

  20. Oh my, I am amazed at how good these are. Thank you so much for sharing!  

  21. 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!

  22. I have almond flour but no coconut flour – is there a good substitute?

  23. These are so delicious! My son asked if I would make them “every day for the rest of his life.”

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

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

  26. Thinking of adding shredded carrots, what do you think?

  27. Hi, coconut is not my thing.  What can I use as a substitute?  Thanks 

  28. 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. 

  29. Can you use frozen bananas for this recipe?

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

  31. Thank you! I am going to make these, could you use regular flour substitute for the almond and coconut? 

  32. 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!

  33. 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!

  34. 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?

  35. 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

    • 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.  

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

  37. Just wondering what to use if you don’t have almond flour or coconut flour?  Do not need gluten free.