Cream Cheese-Stuffed Almond Flour Banana Muffins

Soft, sweet, and filled with a creamy center, these almond flour banana muffins are the kind of breakfast treat that makes a batch of overripe bananas feel like very good news.

There’s something especially comforting about banana muffins baking in the oven. The kitchen starts to smell warm and sweet, and before long, you have a pan of tender muffins ready for breakfast, an afternoon snack, or whenever you want something homemade with your coffee.

These are a little more special than your everyday banana muffin. Almond and coconut flour give them a wonderfully moist texture, while a spoonful of sweetened cream cheese is tucked right into the middle. Break one open while it’s still a little warm, and you get soft banana muffin surrounding that creamy center. It’s easily my favorite part.

They’re also naturally gluten-free and a great way to use very ripe bananas. Make a batch for the week, keep a few in the fridge, and freeze the rest for an easy treat later on.

Why You’ll Love This Recipe

There’s a lot to love about these little muffins, but the cream cheese filling is what really makes them stand out. Instead of frosting sitting on top, the creamy, lightly sweet filling is hidden right in the center, so you get a little of it with every bite.

They’re wonderfully moist. Very ripe bananas add plenty of moisture, and almond flour gives the muffins a soft, tender texture.

They’re naturally gluten-free. Almond flour and coconut flour take the place of traditional wheat flour here.

They make good use of ripe bananas. If you have three bananas getting very spotty on the counter, this is exactly the sort of recipe to save them for.

They’re easy to keep on hand. Store a batch in the refrigerator for breakfasts and snacks throughout the week, or freeze individual muffins for later.

And despite that creamy middle, there’s nothing complicated about making them. You’ll prepare a simple banana batter, mix the cream cheese with the remaining sugar, layer everything in the muffin pan, and bake.

Ingredients You’ll Need

Here’s what goes into these Cream Cheese-Filled Almond Flour Banana Muffins and why each ingredient matters:

Very Ripe Bananas – The star of these muffins! Very ripe bananas bring natural sweetness, plenty of banana flavor, and help keep the muffins wonderfully moist. You’ll need 1 2/3 cups, from 3 medium bananas.
Almond Flour – Gives the muffins their soft, tender texture and makes the recipe naturally gluten-free. Its richness also helps create that moist crumb.
Coconut Flour – Works alongside the almond flour to give the batter structure and soak up some of the moisture from the bananas.
Baking Powder and Baking Soda – These are the leaveners that help the muffins rise and keep them from becoming too dense.
Salt – Just a small amount balances the sweetness and brings out the banana and vanilla flavors.
Butter – Softened butter adds richness and helps create a tender muffin. The recipe only needs 2 tablespoons.
Brown Sugar – Adds sweetness with a little caramel-like depth. It’s divided between the banana batter and the cream cheese filling.
Eggs – Two large eggs help bind everything together and give the muffins structure as they bake.
Vanilla Extract – A teaspoon of vanilla adds a warm sweetness that pairs especially well with ripe banana and cream cheese.
Reduced Fat Cream Cheese – This is what makes these muffins special. It’s mixed with some of the brown sugar and tucked into the center of each muffin for a creamy, lightly sweet surprise in every bite.

Step-by-Step Instructions

Let’s bake!

First, prepare the pan.

Preheat oven to 325°F. Line cupcake tin with liners.

Mash the bananas.

Mash bananas in a bowl, set aside.

Very ripe bananas are perfect here. Once mashed, they’ll become part of the wet mixture and give the muffins their banana flavor and moist texture.

Mix the dry ingredients.

In a medium bowl, combine almond flour, coconut flour, baking powder, baking soda and salt with a wire whisk. Set aside.

Whisking everything together now helps distribute the baking powder, baking soda, and salt before the dry ingredients meet the wet mixture.

Cream the butter and sugar.

In a large bowl cream butter and 1/4 cup of the sugar with an electric mixer.

Add the bananas.

Add eggs, bananas and vanilla; beat at medium speed until thick. Scrape down sides of the bowl.

At this point, you’ll have the sweet banana mixture that forms the base of the muffins.

Finish the batter.

Add flour mixture, then blend at low speed until just combined.

Once the flour goes in, there’s no need to keep mixing. Stop when the batter has just come together.

Make the cream cheese center.

Mix the cream cheese and remaining sugar.

This simple mixture becomes the creamy surprise tucked inside each muffin.

Fill the muffins and bake.

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.

And that’s it! Once they’re baked, you’ll have tender banana muffins with a sweet cream cheese layer waiting inside.

Expert Tips

The riper the bananas, the better. This recipe calls for very ripe bananas, so reach for bananas that are soft and generously spotted rather than firm yellow ones.

Measure your mashed banana. Three medium bananas should give you the required amount, but banana sizes vary. For the recipe itself, stick with the specified 1 2/3 cups.

Don’t overwork the batter. After adding the flour mixture, blend on low only until everything is combined.

Keep the cream cheese in the center. Spoon about 2 teaspoons onto the first layer of batter, then cover it with the remaining batter. That way, the filling stays tucked inside the muffin as it bakes.

Check the muffins rather than relying only on the clock. The baking time is 35 to 45 minutes. Use the recipe’s toothpick test to determine when yours are ready.

Recipe Variations

I love these muffins just as they are, especially because the creamy center already gives them something extra. But if you’re in the mood for a little crunch, nuts are an easy addition.

Top the muffins with chopped almonds, pecans, or walnuts, or mix 1/2 cup of nuts into the batter to turn them into banana nut muffins.

You can also leave the batter completely unchanged and vary what you serve alongside the muffins. Fresh berries, sliced banana, yogurt, or nut butter can make the same batch feel a little different from one morning to the next.

Storage & Reheating

These muffins are especially handy to make ahead. Once cooled, keep them in the refrigerator, where they’ll last for 4 to 5 days.

Want to save them longer? Wrap the muffins individually in plastic wrap or foil and place them in a zip-top bag or container before freezing. Having them wrapped individually makes it easy to take out exactly as many as you need.

For an easy breakfast the next morning, move a frozen muffin to the refrigerator before bed. Once thawed, warm it in the microwave for about 20 seconds.

You can also microwave a muffin directly from frozen. Just give it a little more time to warm through.

Serving Suggestions

I especially like these muffins slightly warm, when the banana crumb is soft and the cream cheese center is creamy. Pair one with a mug of coffee or tea, and you have a simple breakfast that feels a little more special than the usual weekday routine.

For a bigger breakfast or brunch, serve them with fresh berries or sliced fruit, Greek yogurt, and eggs. The muffins bring the sweet element to the table, so they pair nicely with simple savory dishes.

They’re just as good in the afternoon. Have one with tea or coffee for a quick snack, or serve them as a simple dessert when you want something sweet without making a frosted cake or a more elaborate treat.

However you serve them, don’t forget about that cream cheese center. It’s the little surprise that turns a simple banana muffin into something worth making again.

Recipe FAQs

1. How ripe should the bananas be?

Use very ripe bananas for these muffins. The softer and more spotted they are, the better. Ripe bananas add sweetness, moisture, and plenty of banana flavor. Just make sure to measure 1 2/3 cups mashed banana so you have the right amount for the batter.

2. Can I use only almond flour instead of almond and coconut flour?

I don’t recommend using only almond flour. Coconut flour absorbs much more moisture than almond flour, so simply swapping one for the other can change the texture of the muffins. For the best results, stick with the 1 cup almond flour and 1/3 cup coconut flour called for in the recipe.

3. Why is my muffin batter so thick?

A thicker batter is normal with this recipe. Coconut flour absorbs quite a bit of moisture, while almond flour behaves differently than regular wheat flour. There’s no need to add extra liquid. Just mix on low speed until everything is combined and continue with the recipe.

4. How do I keep the cream cheese filling in the center?

Add half of the batter to the muffin pan first, then place about 2 teaspoons of the cream cheese mixture in the center of each muffin. Cover with the remaining batter. Try to keep the cream cheese away from the edges so it stays tucked inside as the muffins bake.

5. How do I know when the banana muffins are done?

Bake the muffins at 325°F for 35 to 45 minutes. Insert a toothpick into the center to check for doneness. If it comes out clean, they’re ready. Since almond flour muffins can brown nicely before the inside is finished, use the toothpick test instead of judging them by color alone.

Cream Cheese-Stuffed Almond Flour Banana Muffins

Tender banana muffins made with almond and coconut flour, with a lightly sweetened cream cheese center tucked inside each one.

Print Pin

Course: Breakfast

Cuisine: American

Keyword: Cream Cheese-Filled Almond Flour Banana Muffins, Easy Cream Cheese-Filled Almond Flour Banana Muffins

Prep Time: 20

Cook Time: 40

Total Time: 1

Servings: muffin

Ingredients

1 2/3 cups very ripe bananas, from 3 medium
1 cup almond flour
1/3 cup coconut flour
2 tsp baking powder
1/2 tsp baking soda
1/4 tsp 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

Instructions

Heat the oven to 325°F and place liners in a cupcake tin.
Mash the bananas in a bowl and put them aside.
In a medium bowl, whisk together the almond flour, coconut flour, baking powder, baking soda, and salt. Set this dry mixture aside.
Using an electric mixer, cream the softened butter with 1/4 cup of the brown sugar in a large bowl.
Add the eggs, mashed bananas, and vanilla. Beat on medium speed until the mixture becomes thick, stopping to scrape down the sides of the bowl as needed.
Add the flour mixture and blend on low speed just until everything is combined.
In a separate bowl, mix the cream cheese with the remaining brown sugar.
Divide half of the muffin batter among the prepared cups. Spoon about 2 teaspoons of the cream cheese mixture into the center of each muffin, then cover with the remaining batter.
Place the pan on the center oven rack and bake for 35 to 45 minutes, until a toothpick inserted into the center comes out clean.