Soft, moist, and topped with a swirl of fluffy frosting, these healthy banana cupcakes with cream cheese frosting taste just like banana bread in cupcake form! They're made with almond flour, ripe banana, and maple syrup, so they're gluten-free and perfect for birthdays, a sweet snack, or even breakfast. If you love my healthy pumpkin cupcakes or my paleo chocolate cupcakes, these banana cupcakes need to be next on your list!

Jump to:
- Easy Gluten-Free Healthy Banana Cupcakes
- Why You’ll Love This Recipe
- Ingredients Needed To Make These Healthy Banana Cupcakes
- How to Make Healthy Banana Cupcakes with Cream Cheese Frosting
- Erin's Expert Tips
- Frequently Asked Questions
- Storing leftovers
- If you liked this recipe, try these!
- Healthy Banana Cupcakes with Cream Cheese Frosting
Easy Gluten-Free Healthy Banana Cupcakes
These gluten-free banana cupcakes start with a simple almond flour batter. First, almond flour, baking soda, cinnamon, and salt get mixed in one bowl. Then, a mashed ripe banana is whisked together with eggs, melted coconut oil, maple syrup, and vanilla in another. Stir them together, scoop into lined muffin tins, and bake until golden.
While the cupcakes bake, whip up a quick cream cheese frosting with Neufchatel cream cheese, powdered sugar, butter, vanilla, cinnamon, and a pinch of salt. After chilling for 30 minutes, it's perfectly pipeable. If you love banana desserts, my classic healthy banana bread is a reader favorite too.
These cupcakes are perfect for birthday parties, baby showers, or a cozy afternoon treat. And if you need more healthy cake recipes like this one, you're going to LOVE my healthy carrot cake or my healthy banana bread muffins!
Why You’ll Love This Recipe
- Tastes like banana bread. Soft, moist, and full of banana and cinnamon flavor.
- Gluten-free. Made with almond flour instead of all-purpose flour.
- Naturally sweetened cupcakes. Plus, maple syrup and banana sweeten the cake.
- Tangy cream cheese frosting. It's light, creamy, and the perfect finishing touch.
- Party-perfect. They're a hit at birthdays and showers!
- Easy to make. Best of all, you just need two bowls and a muffin tin.

Ingredients Needed To Make These Healthy Banana Cupcakes
Here's a little bit about everything that goes into these healthy banana cupcakes with cream cheese frosting:
- Almond flour: Gives the cupcakes a soft, tender crumb and keeps them gluten-free.
- Ripe banana: Adds natural sweetness and moisture. You'll need about ½ cup mashed.
- Eggs: Help the cupcakes rise and hold together.
- Coconut oil: Melted coconut oil keeps them moist. Melted butter works too!
- Maple syrup: Naturally sweetens the cupcakes. Honey works as well.
- Neufchatel cream cheese: The base of the frosting. It's lighter than regular cream cheese.
- Powdered sugar: Sweetens the frosting and gives it a smooth, fluffy texture.
How to Make Healthy Banana Cupcakes with Cream Cheese Frosting
These cupcakes come together in two simple parts: the banana cupcake batter and the cream cheese frosting. First, mix the dry ingredients in one bowl and the wet ingredients in another, then stir them together and scoop the batter into lined muffin cups.
While the cupcakes bake, beat the frosting ingredients until smooth and chill it so it firms up. Most importantly, let the cupcakes cool completely before frosting. Otherwise, the frosting will melt right off!

- Step 1: Preheat the oven to 350°F and line a muffin tin with cupcake liners. Spray the liners with nonstick spray. In a small bowl, mix the almond flour, baking soda, cinnamon, and salt.

- Step 2: In a large bowl, mash the banana. Then whisk in the eggs, melted coconut oil, maple syrup, and vanilla.

- Step 3: Add the dry ingredients to the wet and stir until combined.

- Step 4: Using a cookie scoop, fill the muffin cups about ⅔ full. Bake for 20-23 minutes, until golden brown.

- Step 5: While the cupcakes bake, use a hand mixer to beat the cream cheese, powdered sugar, butter, vanilla, cinnamon, and salt until creamy. Chill the frosting in the fridge for 30 minutes.

- Step 6: Once the cupcakes have fully cooled, frost and enjoy.
Erin's Expert Tips
From my kitchen to yours
- Use a ripe banana. The spottier it is, the sweeter and more flavorful the cupcakes.
- Spray the liners. It keeps the almond flour cupcakes from sticking.
- Use a cookie scoop. It makes filling the cups quick and even.
- Chill the frosting. Thirty minutes in the fridge helps it firm up for piping.
- Cool completely before frosting. Otherwise, the frosting will melt.
Frequently Asked Questions
Below are some common questions about these healthy banana cupcakes with cream cheese frosting.
Yes! Bake them for less time and check for doneness with a toothpick.
Oat flour doesn't work the same as almond flour, and most flours aren't a 1:1 swap. You'd need to adjust the ratio, so I recommend sticking with almond flour.
Melted butter is a great substitute for coconut oil.
Yes, honey should work just fine.
Yes! It just takes a little more elbow grease to get it smooth.
Yes, they're made with almond flour, so they're naturally gluten-free.
Keep them in a sealed container in the fridge for up to 3-4 days.
Storing leftovers
Since they're topped with cream cheese frosting, store your banana cupcakes in a sealed container in the fridge for up to 3-4 days. Let them sit out for a few minutes before eating so the frosting softens slightly.

If you tried this recipe or any other recipes on my blog, please leave a 🌟 star rating and let me know how it went in the 📝 comments below. Follow @erinliveswhole on Instagram and tag me in any of the recipes you make so I can repost them!
If you liked this recipe, try these!

Healthy Banana Cupcakes with Cream Cheese Frosting
Ingredients
- 2 ½ cups almond flour
- ½ teaspoon baking soda
- 1 teaspoon cinnamon
- ¼ teaspoon salt
- 1 large ripe banana mashed (about ½ cup mashed)
- 2 eggs
- ¼ cup coconut oil melted
- ⅓ cup maple syrup
- splash vanilla
- 8 oz Neufchatel or reduced fat cream cheese, softened
- 1 cup powdered sugar
- 2 tablespoon butter softened
- 1 teaspoon vanilla
- ¼ teaspoon cinnamon
- ¼ teaspoon salt
Instructions
- Preheat oven to 350 and line muffin tin with cupcake liners. I always also spray my muffin liners.
- In a small bowl, mix together almond flour, baking soda, cinnamon, and salt.
- In a large bowl, mash banana. Whisk in two eggs, coconut oil, maple syrup and vanilla.
- Add dry ingredients to wet and stir until combined. Using a cookie scoop, scoop into muffin tin filling ⅔ the way. Bake for 20-23 minutes or until golden brown.
- While baking, prepare cream cheese frosting. Using a hand mixer, blend together cream cheese, powdered sugar, butter, vanilla, cinnamon, and salt until creamy. Chill in fridge for 30 minutes.
- Frosting cupcakes once cake has fully cooled and frosting has firmed up slightly.
Nutrition
Per serving. Nutrition is an estimate.
Leave a star rating below and tag me on Instagram so I can see your creation!
Rate This RecipeRecipe by Erin Morrissey and Photos by The Mindful Hapa











Phyllis Conway says
These are delicious and I make them often enough that anyone who knows me has had the pleasure to taste them too!!!!
If I want to try to make these for someone who is vegan, how do I adjust the ingredients and/or preparation and baking?
Thank you,
Phyllis
Phyllis says
How may I use these ingredients to make cookies?
Estefania Rodriguez says
Hi,
I make these ALL the time for my toodler and he loves them. We are celebrating his birthday next month and would love to bring to school. However, school is nut-free. Is there a good and healthy substitute for the almond flour that doesn't compromise taste and texure?
Rychelle says
This is the most delicious recipe! The whole family loves them. Thanks Erin 🙂
Erin says
Hi Rychelle, so happy you all loved them so much! 🙂
Sam says
Hello Erin! I loved this recipe. Is it okay if I use the ingredients for my novel? I can include you and this site in the works cited page!
Erin says
Hi Sam, sure! So glad you liked the recipe. 🙂
Nanajee Travels says
If you're in the mood for a sweet snack that's both healthy and delicious, these Healthy Banana Cupcakes with Cream Cheese Frosting are a must-try! They sound perfectly rich and make for a great dessert or mid-day treat. Plus, being ready in under an hour makes them super convenient—can't wait to whip up a batch!
Erin says
Hi Nanajee, so happy you loved them so much! 🙂
Melissa says
Hi, I want to make mini cupcakes, do you know if the recipe should be adjusted or how much time it should bake for?
Erin says
Hi Melissa, I'd just take the time, cut it in half and then continue to test them with a toothpick to see if it comes out clean. Once it does, you're done! Let me know how they come out!
Stephanie says
Can you use oat flour instead?
Erin says
Hi Stephanie, hmm nut flours don't work the same, but feel free to give it a try and just triple check the ratio since most flours aren't 1:1.
Emily Hickman says
What’s the best oil substitute if we can’t use coconut?
Erin says
Hi Emily, you can use melted butter! Let me know how they come out!!
Suzanne says
Hello! Can I make the frosting without a hand mixer?
Erin says
Hi Suzanne, yeah that should work! You'll just have to work to make it smooth. Let me know how it comes out! 🙂
Liz H says
Would honey work instead of maple syrup?
Erin says
Hi Liz, that should be fine. Let me know how they come out!!
Ashley says
Wow! Made these for my son’s first birthday and he LOVED them! They were soft, moist, and delicious! All the other kiddos at the party gobbled them up as well, having no idea they are healthy! Thanks for such a great recipe! Will definitely make these again!
Erin says
Hi Ashley, so happy they were such a hit!! 🙂