Healthy Peanut Butter Chocolate Banana Muffins
Healthy chocolate peanut butter banana muffins are moist, fluffy and the perfect amount of chocolate flavor! Made with whole wheat flour, apple sauce, and peanut butter, enjoy these healthy muffins for breakfast, dessert or a snack.

My blog is slowly transforming into a baking blog and I’m more than ok with it… so I hope y’all are too. I’m finding out that muffins are my favorite thing to bake/make in general. They also might be my favorite thing to eat as well. 😉
Healthy muffins are so versatile! You can have them for breakfast, an afternoon snack, dessert, you name it.
Pretty much all of my favorite muffin recipes involve chocolate chips (i.e. Sweet Potato Chocolate Chip Muffins, One Bowl Chocolate Chip Zucchini Muffins, Dark Chocolate Raspberry Banana Muffins… you get the idea) so I figured I’d keep the trend going.
I love warming them back up in the microwave, letting the chocolate chips get all melty again and topping with a scoop of vanilla frozen yogurt.
Seriously NOTHING better. This way it almost tastes like you’re eating chocolate cake instead of a muffin!

If you follow me on Instagram, you already know my love for all things peanut butter runs deep. It’s in my bio, after all.
How I didn’t have a peanut butter banana muffin recipe already is beyond me!
Moist, chocolatey, and guilt-free, these clean-ingredient muffins combine whole-wheat flour, applesauce, peanut butter, and a hint of cocoa for a low-added-sugar treat you can enjoy any time: breakfast, lunchbox snack, or dessert. (Gluten-free and vegan variations included below.)
Thankfully I came to my senses because these muffins are next level. If I do say so myself. 🙂
After a couple of attempts, I’d say I achieved the perfect balance of sweetness. The banana flavor pairs so well with the rich peanut butter and semi-sweet chocolate chips.

How to make low added sugar muffins
I love baking with bananas because they offer their own natural sugars which really limits how much added sugar you need.
I’m all about balancing those blood sugar levels, yall. Read more about my nutrition coaching approach here.
Baking with sweet potatoes helps limit the amount of sugar baked goods need, too!
I have several recipes that use sweet potatoes as the base (I.e. Dark Chocolate Flourless Sweet Potato Brownies, Sweet Potato Banana Bread, and Chocolate Chip Sweet Potato Muffins) and they are some of my posts popular recipes.
Ingredients For Clean & Healthy Peanut Butter Chocolate Banana Muffins
- Bananas – make sure they are ripe.
- Brown Sugar – or Coconut sugar
- Unsweetened Apple Sauce
- Natural Peanut Butter – only use creamy peanut butter, not crunchy.
- Whole Wheat Flour and All-Purpose Flour
- Butter
- Cocoa Powder
- Salt
- Baking Soda and Baking Powder – this is what makes these delicious muffins tall and fluffy, so make sure they aren’t expired.
- Chocolate Chips – I like using semi-sweet, but you can use milk or dark chocolate.
- Egg
You Will Also Need:
- Muffin Tin
- Muffin Liners
- Mixing Bowls
- Measuring Cups
- Rubber Spatula
P.S. Head over to my Amazon shop to see my favorite baking ingredients, utensils, and equipment!

How to Make Chocolate Peanut Butter Banana Muffins
Move your oven rack to the center and preheat to 375 degrees. Line a muffin pan with paper liners and set aside.
Use a fork or potato masher to mash the bananas in a large mixing bowl.
Add the sugar, egg, butter, applesauce, and peanut butter to the mashed banana. Mix just until combined.
Stir the remaining dry ingredients into the wet ingredients until incorporated.
Use a rubber spatula to gently fold in the chocolate chips.
Scoop the muffin batter into the prepared pan, filling each muffin cup 2/3 of the way full. If desired, add a few more chocolate chips on top of each muffin before baking.
Bake for 20 minutes or until a toothpick comes out clean.
Remove the muffins from the oven, and transfer to a wire rack to cool.

Substitutions and Variations
Almond butter – can be swapped for the peanut butter, but obviously will have a different flavor.
Peanut butter chips – use these if you really want more peanut butter flavor.
Mini muffins – use a mini muffin pan instead of regular. Remember to keep an eye while baking. Because they are a little bit smaller, they will take less time to bake.
Chocolate chunks – instead of chocolate chips, you could chop baker’s chocolate or use cacao nibs.
Gluten Free Flour – Make sure it’s 1:1 ratio gluten free flour
Tips for Making
- Do not over mix the muffin batter. This will lead to tough and dense muffins.
- For best results, use brown, spotty bananas. Extra ripe bananas adds the most sweetness.
How to Store
Once the chocolate peanut butter muffins have cool completely at room temperature, keep leftovers in a tightly sealed container for up to 3 days in in the refrigerator.
Can I freeze chocolate banana muffins?
Freeze individually in plastic wrap for up to 2 months if desired.
I hope you all enjoy these easy, healthy peanut butter chocolate muffins as much as we did!
This recipe makes 12 large muffins and is ready in about 30 minutes from start to finish.
Be sure to tag me on Instagram when you make these muffins so I can share your creations on my stories 🙂
Happy Sunday!
[ PIN ME FOR LATER ]

Why should you bake with overripe bananas?
Overripe bananas are the best for making banana bread because they taste sweeter! They may also be moister, which is perfect for baked goods.
The brown spots on a very ripe banana indicate that even more starch has been converted to sugar.
What can I use instead of peanut butter?
You can swap out peanut butter for any of your favorite nut or seed butters. Just be sure there are no added oils or sugar!
More peanut butter and chocolate muffin recipes you will love!
- Peanut Butter Protein Muffins – gluten and dairy free
- Vegan Banana Chocolate Chocolate Chip Muffins
- Oatmeal Chocolate Chip Muffins
Chocolate Peanut Butter Banana Muffins
Ingredients
- 3 Ripe Bananas Mashed VERY well (basically blended)
- 3/4 Cup Brown Sugar
- 1 Large Egg
- 1/3 Cup Unsweetened Apple Sauce
- 2 Tbsp Melted Butter
- 1/2 Cup Peanut Butter Creamy
- 1/2 Cup Stone Ground Whole Wheat Flour See post for which one I use
- 1/2 Cup all purpose flour
- 1/2 Cup Unsweetened Cocoa Powder
- 1/2 Tsp Salt
- 1 Tsp Baking Soda
- 1 Tsp Baking Powder
- 1 Cup Chocolate Chips
Instructions
- Preheat the oven to 375°F and position a rack in the center. Line a muffin tin with baking cups and set it aside.
- In a large bowl mash the bananas with a fork or potato masher (i usually throw them in my mixing bowl and mix on low for a minute or so) then mix in the sugar, egg, applesauce, butter and peanut butter until combined. Stir in the flours, cocoa powder, salt, baking soda, and baking powder over the banana mixture.
- Mix lightly with a rubber spatula to combine. Fold in chocolate chips. Do NOT over-mix!
- Using a spring-loaded ice cream scoop or spoons, divide the batter between the prepared muffin cups and bake them for about 20 minutes until a toothpick inserted into the middle comes out clean.
- Transfer them to a rack to cool. Store muffins in an airtight container in the fridge for up to 3 days.
Just made these today… They are absolutely delicious and easy to make.. I subtituted the brown sugar queen Monk fruit sweetener to lower the sugar content.
Just made these and they are PERFECTION. Makes me happy knowing there is some Applesauce and bananas in there that my picky kids won’t eat by itself. I will be making this recipe on repeat! Thank you!
These have been my very favorite muffins since I first made them in 2020 during quarantine. Today I actually craved them but realized I was out of banana. A little improvising and again just delicious. I used extra unsweetened applesauce and pumpkin puree to replace bananas along with all other ingredients. They were moist, fluffy and delicious. I just can’t believe I haven’t sent in a review earlier but wanted to make sure today to give you a big thank you for such a yummy healthy-ish treat.
Subbed stevia for brown sugar and zero sugar chocolate chips. Carb count is 26g for one muffin if you make 12 muffins. I had to figure them for my T1 son so i figured i would share!
Hey, can you share the nutrition info. for these muffins? They’re so good!! Thanks!
I made these for my family yesterday morning and everyone loved it! My family had eaten all of them by the time I went for seconds! I’m going to make them again today or tomorrow, and was wondering if I made a double batch if I could freeze some of the batter? These are definitely a new family favorite. Thank you!
Have you tried making these with Almond Butter instead of Peanut Butter for those with peanut allergy?
Yes! You can use any nut or seed butter.
Thank you for the comment will try almond butter next time!
Very delicious – made them to bring to a brunch & they were all gone! Glad I saved one for my husband at home!
So happy to hear it!! Let me know what you think of the almond butter swap! 🙂
Delicious! Instead of apple sauce I used Greek Yogurt and instead of the regular flour I used half Whole Wheat and half Almond Flour, they came out so moist! I will definitely be making them again.
I made these so many times when I was pregnant. Love how decadent they taste with whole ingredients! We’re currently waiting for results of allergy testing for my 6 month old and I just successfully made this allergen friendly. Switched the flour for 1:1 King Arthur GF flour, used vegan butter (earth’s best soy free), and omitted the peanut butter. I doubled the apple sauce to ensure I’d have enough moisture and they turned out phenomenal! (Oh, and I used dairy free chocolate chips!)
Sooooo yummy!! I’ve made them countless times and they never fail. Definitely a go to recipe!
Best most delicious muffin I’ve made all my favorite ingredients and yet on the healthy side , I make them all the time just a bit smaller so I get 24 OR I make them mini so I get way more. My family loves them too
I have to say these are the BEST cupcakes I have made.
They are so moist and yummy. I used whole wheat flour for the recipe only. It turned out super! And I love how there is in oil in them.
I have made this recipe quite a few times. It is always a hit, no matter who you are sharing with. I love the balance between a sinful treat and a healthy one. These come out looking beautiful each time.
These are insane! Just made them with my little girl and we are obsessed already, I didn’t have any wholewheat flour so just used all plain and they came out amazing.
I would question how ‘healthy’ they are but I am not complaining at all. The texture and flavour are perfect thank you!
Somehow I forgot the brown sugar, but I did everything else exactly as listed and they are great! I looooove sweets and couldn’t tell this was missing sugar!
All I can say is WOW!!!
they were amazing and healthy! what more could one ask for !
Thanks again for another great recipe. I have already made this a couple of times. It is becoming a family and friend favorite!!
Do you know if these can be frozen? They sound good.
They can!
This looks really good. I personally love banana muffin, but I haven’t tried peanut butter chocolate banana muffin. Will surely try this one. Thank you for this!
Yay! It’s a winner for sure! Let me know if you do! 🙂
These came out excellent!
Thank you so much! I’m glad you enjoyed them!
These were delicious. I used a monks fruit sweetener and no chocolate chips bc I have a sugar free kid but that sweetener can dry out baked goods but these were still moist and delicious. I did however get 12 full sized and almost a whole tray of minis (bakes only 10 minutes). I’m not complaining because the more the merrier I say but that might affect those who are saying they are too calorie dense!
So glad you enjoyed them!! Thanks for letting me and future readers know about these swaps! I will definitely look into adjusting the amount this recipe makes based on your comment. Have a great day!
Would you be able to add more peanut butter to the recipe without altering the consistency too much? I can’t taste much of it and I love peanut butter!
Hi! I’m not sure because I have only made the recipe as listed. Feel free to give it a try!
Perhaps add peanut butter chips instead of chocolate chips? That would be good!
You can add whatever chips you like!
They taste amazing but when calculating the calories this is almost 300 calories for one muffin. I guess I would agree healthier ingredients.
So glad you liked them!
I followed exactly as listed except for the whole wheat flour I used all purpose flour all around so 1 cup total. These are by far my favorite muffins. Not too sweet but just perfect and you taste all the flavors. Mine came out light and fluffy as well! My husband and I already made a second batch. They are perfect for a quick breakfast on the go!
Thank you so much for the awesome review! I’m so glad you all love them as much as we do! Happy baking 🙂
My cupcakes came out clumpy Like I should have put oil in them. Maybe I did something wrong?
Hi! Sorry to hear that! The butter, applesauce, and peanut butter should have kept them moist. Did you accidentally leave any of that out?
What do I do if I want to replace the all purpose flour for self rising flour? Do I just replace the same amount but remove the additional baking soda and salt?
Hi Jessica! I’ve only made the recipe as listed so I’m not sure how self-rising flour would work. Sorry I’m not a better help!
You mention Greek yoghurt but I can not see it in ingredients list. Do you use Greek yoghurt or not?
Hi! I’m not sure where in the ingredient list you are seeing that but no you do not!
Can you use all purpose flour instead of whole wheat flour for the entire recipe?
I’ve only made them as listed but I’m pretty sure that would work just fine 🙂
All I taste is banana 🙁 but they are nice and moist
Hello Desiree
Did you try them with all purpose flour? I am wondering how they worked?
Hi Gail, I made this recipe as listed, with the exception of all purpose flour in place of the whole wheat flour since I didn’t have any whole wheat flour on hand (so 1 cup of all purpose flour total). They turned out great for me!
These look absolutely amazing and I cannot wait to try them!
Made over 30 and love them, wondering how many calories per muffin?
Yay! I’m not sure — I don’t count calories but you can easily add the ingredients into a calorie generator online if you’d like 🙂
Can these be baked in a mini muffin pan?
I don’t see why not! I never have, but I would just reduce the baking time and keep an eye on them 🙂
If I don’t have applesauce what else do I use?
You could try more mashed banana or greek yogurt!
Yum! Love the fact they are healthy too!
those look beautiful but a bit too decadent for me! bravo on the great photos and pins on pinterest
Joy at The Joyous Living
Made these again!!
Everyone loves them. Peanut butter, bananas and chocolate are a great combination .
Really good. Great combination. Made per recipe. Will be making these again and again!
Yay! So so happy to hear you enjoyed them and will be making them again. Thank you for taking the time to leave a rating a review! 🙂