Healthy Chocolate Chip Pumpkin Muffins
Super moist and lightly sweetened with honey, these healthy chocolate chip pumpkin muffins make the perfect fall breakfast or on-the-go snack! Made all in one bowl with coconut oil and white whole wheat flour.
The Best Healthy Pumpkin Muffins
Soft and lightly spiced healthy pumpkin chocolate chip muffins are a favorite during this time of the year. They make the best take-and-go breakfast and can double as a snack or even dessert.
They are sweetened only with honey and bananas, and instead of white flour, made with white whole wheat flour. And did I mention you only need one bowl, a whisk, and a spoon to make them? That’s right! No mixer is required.
Make a double batch to enjoy now and freeze for later. These pumpkin muffins keep well in the freezer for up to 3 months.
It’s All About the Right Ingredients
A big part of what makes these healthy pumpkin chocolate chip muffins so amazing is simply a combination of ingredients.
Even though you can make substitutions to some of the ingredients, which I do cover below. But for best results, follow the recipe as written:
- Coconut Oil: Refined coconut oil is neutral and ideal to use in this recipe. It has no distinct coconut taste or aroma like virgin or unrefined coconut oil.
- Honey: Honey provides sweetness to the muffins. Maple syrup can be used as a substitute.
- Eggs: You’ll need two large eggs for this recipe.
- Bananas: Bananas make the muffins sweet and extra moist. Make sure to use ripe bananas and measure out the banana mash before adding it to the batter.
- Pumpkin Puree: Canned pumpkin is the same as pumpkin puree. It simply means 100% pureed pumpkin. I had a reader ask if pumpkin pie filling and/or mix can be used instead. Normally pumpkin pie filling has added sweetener and other ingredients, therefore, I do not recommend it.
- Milk: I used dairy milk for this recipe but non-dairy milk, such as almond milk will work as well.
- Pumpkin Pie Spice: Also known as pumpkin spice, is a spice mix of cinnamon, ginger, nutmeg, cloves, and allspice.
- Baking Soda: It helps the batter rise and make the muffins light. I do not recommend a substitute.
- Vanilla Extract: Vanilla enhances the flavor of the muffins and makes them taste yummy.
- Salt: I like to use kosher salt but a sea salt is a great option too.
- White Whole Wheat Flour: Is a great middle between all-purpose flour and whole wheat flour. It’s mild in flavor and pale in color than whole wheat flour as it’s made with a different variety of wheat. But the nutritional value is similar.
- Chocolate Chips: Semi-sweet or dark chocolate chips work. Keep in mind if using semi-sweet chips, the muffins will be sweeter.
Can You Make These Muffins Gluten-Free?
Yes! Simply use a gluten-free all-purpose flour blend. Some of the readers had luck with Bob’s Red Mill 1-to-1 Baking Flour, as well as almond flour.
I personally made these pumpkin muffins with oat flour and they were as equally delicious.
How to Make Healthy Pumpkin Chocolate Chip Muffins
Grab a large mixing bowl, a whisk, and a wooden spoon, and let’s make the batter:
- Whisk together the coconut oil and honey. Then add in the eggs.
- With a wooden spoon, stir in the bananas, pumpkin puree, milk, pumpkin pie spice, baking soda, vanilla extract, and salt.
- Gently stir in the flour just until combined. Do not overmix. And lastly, fold in the chocolate chips.
- Grease a 12-cup muffin pan and divide the batter evenly between the cups, filling all the way to the top.
- Bake for 5 minutes at 425 F, then keeping the muffins in the oven, reduce the oven temperature to 350 F, and bake for additional 17-20 or until toothpick inserted in the middle comes out clean. Remove and cool on a cooling rack.
To Store Muffins
Pumpkin chocolate chip muffins will keep at room temperature for up to 3 days. Thereafter, keep them stored in the refrigerator in a sealed container.
These muffins also keep well in the freezer in a freezer-safe bag or container for up to 3 months. Simply defrost individual muffins overnight in the refrigerator and then for a warm, just baked taste, pop them into a microwave for a few seconds or until gently warmed through.
Leftover Pumpkin Puree?
Here are more recipes to make with canned pumpkin puree:
Video: How to Make Healthy Chocolate Chip Pumpkin Muffins
Watch step-by-step on how to make these easy healthy pumpkin muffins.
Healthy Chocolate Chip Pumpkin Muffins
- Prep Time: 12 mins
- Cook Time: 25 mins
- Total Time: 37 mins
- Yield: 12 1x
- Category: Dessert
- Method: Baking
- Cuisine: American
Super moist and lightly sweetened with honey, these chocolate chip pumpkin muffins make the perfect fall breakfast or on-the-go snack! Made all in one bowl with coconut oil and white whole wheat flour.
- 1/3 cup coconut oil, in liquid form
- 1/2 cup honey or maple syrup
- 2 large eggs
- 1 cup mashed ripe banana, about 2-3 bananas
- 1 cup pure pumpkin puree
- 1/4 cup milk
- 2 tsp. pumpkin pie spice
- 1 tsp. baking soda
- 1 tsp. vanilla extract
- 1/2 tsp. kosher salt
- 1 3/4 cups white whole wheat flour, measured correctly
- 1/2 cup chocolate chips, semi-sweet or dark chocolate
- Preheat the oven to 425 degrees F.
- Grease 12 cup muffin pan with non-stick cooking spray or if using liners, line with liners.
- In a large mixing bowl, whisk coconut oil and honey. Whisk in eggs.
- With a wooden spoon, mix in the mashed banana, pumpkin puree, milk, pumpkin pie spice, baking soda, vanilla extract, and salt.
- Add the flour and mix just until combined. Fold in the chocolate chips.
- Spoon the batter evenly into the prepared pan. You should be able to fill all 12 muffin cups.
- Bake for 5 minutes at 425 F degrees, then keeping the muffins in the oven, reduce the oven temperature to 350 F degrees, and bake for additional 17-20 or until toothpick inserted in the middle comes out clean.
- Place the muffin pans on a cooling rack to cool. Store cooled muffins, covered, at room temperature for up to 3-4 days.
- Ingredient Substitutions: See post for all substitutions, including gluten-free options.
- Serving Size: 1 muffin
- Calories: 259
- Sugar: 21.6 g
- Sodium: 218.2 mg
- Fat: 9.8 g
- Carbohydrates: 40.5 g
- Protein: 4.4 g
- Cholesterol: 31.1 mg
Keywords: pumpkin, fall, healthy
I’m looking forward to making these. The reviews and comments look amazing. I typically stick to the recipe, but I appreciate that you provide swaps as I’m trying out gluten free recipes.
Throughout the comments, I didn’t see anyone ask about swapping agave for the honey/maple sugar. What are your thoughts? Would agave work for a lower glycemic index? I have both honey and maple syrup, but I’m wondering about baking with agave. Thank you!
Hi Deb: Honey can be replaced by directly substituting it with agave in equal measure. Hope that helps! Let me know how they turn out for you.
They turned out perfect with the agave! Thank you for the response. I swapped equal measurement as you recommended and they tasted the same as when I made them with honey. Perfectly moist and delicious.
I made mine gluten free with a mix of almond and oat flour. I used 1 cup oat flour and 3/4 cup almond flour. I have not tried them with whole wheat flour yet. The gluten free version is phenomenal. I’ll need to stock up on canned pumpkin so I can make these all year!
Thank you for the great recipe!
I love these so much. They’re amazing! I gave some to a friend who doesn’t usually like pumpkin treats and she loved them. I’ve switched out pumpkin for sweet potato too and they’re just as delicious!
Thank you for this recipe! I have made twice now and the fam loves them! I substituted apple sauce and almond flour on the second go and they turned out just as delicious as the original recipe. 🙂
Can I substitute the wheat flour with all almond flour or do I need to use it in combination with another flour?
I’ve never tried making these with almond flour but I did with oat flour and they turned out great! Simply substitute the same amount of oat flour of white whole wheat.
Thank you! If I don’t have pumpkin pie spice, can I just use 2 tsp cinnamon or would that be too much?
It should be okay.
Hubby just requested these and it’s not fall so that pretty mucha sums up how yummy these are!! We love these and make them for family and friends ALL THE TIME. We like to use maple syrup instead of honey but I’m sure both are just as delicious.
So happy to hear that!
These are the best healthy muffin. This is the second year I’ve made them for holiday parties and they are a hit again! I use my own parchment paper as muffin cups and i don’t need any PAM or extra oil for the pan. I have cut back the oil to 1/4 cup as most of it was ending up in the muffin pan. Also I used 1/4 peanut butter chips and 1/4 chocolate chips and it was a nice variation. Next time I will try adding more allspice or pumpkin pie spice. Thanks for the recipe!
Would it be possible to use coconut flour instead of wheat flour?
I’ve never tried it with coconut flour so I can’t answer with certainty.
Thank you for this recipe! I love all things pumpkin and made these for my son (9 yo) and I. He raved about them. Best ever muffins he said and I make a lot of muffins.
I substituted applesauce for the bananas bc we didn’t have enough and I also substituted canola oil for the coconut oil. Yummy!
Everyone in our house LOVES these muffins! Instead of chocolate chips I use peanut butter chips in the mix and I sprinkle some on top and it is sooo good! Shared this recipe with some friends and they all agree that these muffins are the best and pretty healthy!
Thank you Amanda! So happy to hear you enjoyed the muffins.
These turned out so well! They were so fluffy. I didn’t have enough banana but so I made up the rest of the cup with maple syrup and they were great. Thanks for the recipe!
That’s great! Thank you Emma for your feedback.
This is a recipe that has been on repeat in my household, SO good
I’m not one to make healthy versions of baked goods; they almost never taste as good. But I decided to make an expectation with this recipe, to feed my toddler a healthy breakfast. These were fantastic! They do not taste like a healthy version of a regular muffin at all. Light and fluffy, and a good muffin-y texture. Next time I’ll leave out the chocolate chips, because I don’t think we’d even miss them.
A few changes I made based on the reviews – I added an extra tsp of pumpkin pie spice, sprayed the muffin liners with PAM, and used while wheat pastry flour. Delicious! I also froze most of them for easy breakfasts – just 25 seconds in the microwave will do it.
Thank you Amy! I’m so happy to hear that.
I made these with a gluten free flour/oat flour combo, and with no chocolate chips as I had none. Turned out great, next time I will add raisins!
(I also didn’t have pumpkin pie spice, so added a mix of cinnamon/ginger/allspice/nutmeg)
Thank you for a great recipe ‘base’!
Thank you for this great, healthy recipe! I was using a similar recipe that didn’t have banana, and I always added cranberries to it, so I will be trying that next week once I get some more baking bananas and cranberries!
This batch, I needed to use butter as I didn’t have any coconut oil left. It made 20 muffins and they sunk a bit once I took them out of the oven. But the taste and texture is great! Will definitely be making these again. Will also be trying them as mini muffins with the cooking directions someone posted in the comments.
WOW this recipe is good. Delicious, light, moist. I made it without choco chips and my toddler and I are LOVING it. Just ate two right out of the oven—sorry not sorry.
I just made these and they were PERFECT! I am bookmarking as my go-to muffin recipe. I subbed 100% whole wheat flour and it didn’t make any difference at all, they were light and so moist and delicious. THANK YOU for this recipe that doesn’t make me feel bad because it doesn’t have cups of refined sugar or tons of butter! <3
So happy to the recipe was a success. Thank you Serena!
Thanks for the recipe! I just made these and they were amazing. I didn’t have white whole wheat flour so I used unbleached white flour instead. I also didn’t have enough honey so I substituted maple syrup instead. The muffins tasted great, the only issue was that they were a little gooey at the bottom and completely stuck to the liners. Anyone else have this problem? Not sure if I did something wrong or if one of my substitutions was the culprit. Next time I’ll skip the liners and see what happens.
Glad you enjoyed these. I would give the liners a quick spray next time to ensure nothing sticks.
I added double the pumpkin spice and it was super bland to me idk what I did wrong ????????
Hi Lizzie…I’m not really sure. Two teaspoons of pumpkin spice should be more than enough.
I just made these with my 5 year old – total hit and this kid is picky as picky can get! I love how easy they were to make and that I didn’t have to bust out the mixer! Going to double the batch next time and freeze some.
Thank you! So happy to hear that!
These muffins are delicious and surprisingly moist and tender. Thanks for a great recipe!
These are the absolute BEST! My husband and I ate fairly healthy and our friends do not. I always make these as a “dessert” for them and everyone RAVES about how good they are. Every person is always so shocked when I share the awesome ingredients. Thank for this recipe! So so good!
Thank you Hayley! I so appreciate your feedback.
I’ve made these many times and they always turn out SO well. I use whatever flour I have at the time (have tried whole wheat and all-purpose), and whatever oil (I’ve tried coconut and vegetable). I have also tried adding vanilla protein powder to them (just one scoop) and they turned out great too! Love these. By far my favorite pumpkin muffin recipe!
Thank you Chelsea! Love that you are enjoying these pumpkin muffins. Thank you for the feedback!
Cannot stop eating these! The best pumpkin muffins I’ve ever made! I used regular whole wheat flour and they turned out amazing! They are especially better when you wait a day to eat them so the flavor can sit and they become more moist. I am for sure making another batch tomorrow as we have already eaten all of them! I had some left over batter and used it to make about 10 mini muffins to go along with the normal sized muffins, my 2 year old son loved them and begged for them! Pumpkin in March is perfectly fine with me! 🙂 Thank you for this amazing recipe!
Megan thank you ! That’s so good to hear that you love these pumpkin muffins, especially in March 🙂 I really appreciate your feedback.
These are the BEST! I tried a similar recipe that called for Brown sugar instead of Banana and they were kind of yucky! These however are AMAZING! Thank you for the great recipe! I did use cupcake liners but next time I’ll just put right in the pan with non stick spray since they stuck to the paper. My own fault though! Just wanted others to know! Thank you again!
Yeay! Thank you Mandy. So glad you enjoyed them.
I have made these a good three or four times now. I would be careful not to use overripe bananas, as the intense banana flavor will overpower the pumpkin, transforming this recipe into a banana chocolate chip muffin (with hidden pumpkin for fiber). That said, the banana muffin alternative is still just as delicious! Some other notes are to make sure that the coconut oil is fully incorporated with the honey, or there will be a strange aftertaste. Thank you for the recipe, Katya!
Thank you Nicole! I appreciate your feedback and glad that you’re enjoying these muffins.
I just made these and they were delicious! Thank you so much for sharing this recipe 🙂
Thank you Taylor! Appreciate your feedback.
SO good. Moist, flavorful and not too sweet: highly recommend! Worked well with almond milk too.
Thank you Chelsea!
Just made these this morning! They tasted amazing and I was craving something with pumpkin. I didnt have wheat flour so I used regular flour and used less. I didn’t have enough honey so I used raw sugar and not a full half cup. We also just used up the milk so I just used half-and-half turned out moist. I also adjusted the time I baked them at 375 for 23 minutes.
Thank you Michaela! They are so good, year round 🙂 So glad you enjoyed them.
these muffins are awesome! My whole family loves these.
Hi Katya! Great website! I have a blog as well.
How did you get the nutrition facts box? Is that an add-on? I’m making these muffins and blogging about it. I’m sure you’ll get some more hits afterwards!! Thanks!!
Hi Amanda: thank you! I hope you enjoy the muffins. It’s a plug-in through wordpress called nutrifox. Hope that helps!
Thanks!!! So many plug-ins!! Good to know!!!
These are delicious!! I’ve made them four times in the last month, mini muffins and full size. I can’t wait you try some of your other recipes. Five stars- Thank you!
Thanks so much Laurie!
Hi! I only have regular whole wheat flour. Would that be ok to use? Or do I need to make any changes if I use that type of flour?
Hi Sharlene: whole wheat flour is more denser and heavier , therefore , you will need to use less. I can’t really comment on how much exactly as I have not tried it with whole wheat flour only.
Hi Melissa…hmmm never tried sweet potatoes in dessert recipes, so I can’t really even give you a good answer. But if you do try it, please let me know! Hope you enjoy these.
Can’t wait to make these muffins. Have you ever used sweet potatoes instead of pumpkin? If not do you think it would work well?
GREAT RECIPE! My husband said this is one of the best muffins he has ever had! They were wonderful and made exactly as is. Thanks for the great recipe – so glad I tried it!!
Thanks so much Stephanie! So glad you loved it!
Delicious!! I just made these tonight. I omitted the banana because ours we’ren’t “ready” for baking with. I doubled the recipe and added greek yogurt in place of the banana. I didn’t use vanilla, used white flour, and mini chocolate chips, I also didn’t have pumpkin spice so I substituted nutmeg and cinnamon. I was able to make 48 mini muffins, and 12 regular muffins. These muffins are phenominal and my house smells amazing. Thanks so much for the recipe.
Thanks Melissa! So glad you enjoyed them.
Absolutely delicious! They stayed moist and soft. I did top them with a dollop of cream cheese frosting to make them more of a dessert.
Oh yum! That sounds so good. So happy you loved them 🙂
Made these last night. Very tasty for a healthy muffin.
My three year old and I just made these! They are in the oven as I’m typing and my house smells amazing!! We forgot to add the vanilla, so I hope they still taste good. They are looking fantastic so far!!
I hope both of you enjoy these! Thanks so much for your feedback.
My 6 year old came home from school and had two. She said these are her new favorite muffins. They were delicious, even without the vanilla. I did use gluten free baking mix, due to allergies. This is definitely a keep! I’m so glad I found your blog! Thank you!
That’s awesome Nicole! Thanks so much!
These were delicious! My 2.5 year old and I made them together and had so much extra batter we used it for thick, fluffy pancakes!
I added a little brown sugar and pie spice on top each muffin which gave the extra touch on top.
Thank you for the great family recipe!
Oh yum! Love the pancake idea..something my kids would love too 🙂
Beautiful muffins! I made them as mini muffins. Baked for 12 minutes (3 at 425 F and 9 at 350 F). With six pairs of little hands at home looking for a quick snack or breakfast, these are the perfect size. Two bites and no waste on the breakfast table. Thanks again!
That’s so great! I’m such a fan of small bite size sweets 🙂
Hi! How many mini muffins were you able to make with this recipe? Did you use mini chocolate chips or regular sized ones? If you used mini ones, how much? Thanks in advance!
I also forgot the vanilla but they were still delish. 400 (convection oven) was way too much. Muffins were scorched and uncooked in places. I will try 350 next time, which is what all of my other muffin recipes call for. Great recipe otherwise. Easy to adjust ingredients
You only bake at 425 for 5 minutes and 350 for the remainder of the time.
Thank you for this tip!!
And thank you, Katya, for this amazing recipe!
I got 36 mini muffins out of this
I literally can’t stop making these since my first time making them over 2 weeks ago. I loved the muffins so much I made a cake out of them for my daughters 3rd birthday. So much healthier and more delicious than any store bought cake I would’ve ended up buying. This recipe is seriously life changing and I will probably be using it forever!! Thank you!!
Christina you’re so sweet! Thanks so much for such a nice comment. So glad you’re enjoying the muffins.
I made these this morning and first I would like to say thank you. Muffins are our go to breakfast and we just polished off the last batch of banana muffins and I had three ripe ones staring me down on the kitchen counter. I won’t eat them once they are quite spotted so I have to bake them. Today I didn’t want banana muffins, I really wanted pumpkin chocolate chip muffins. I was looking for a healthy version, not the same old recipe written fifteen different ways. I came across your recipe with both, viola! I also am new at the coconut oil and was happy to see that as well. The maple syrup was the triple bonus, I was sold. I made these as you wrote the recipe with the always exception of GF flour, my love cannot have wheat. The flavor is delicious, I love it! The texture of mine, not so great. I know the flour makes a huge difference and we are used to that but they were too mushy inside no matter how long I baked them. I want to make the necessary changes so they come out as right as possible. Less oil, no milk, less banana?????? Any suggestions. This is a great tasting muffin, thank you again
Hi Kimberly: so glad you enjoyed the muffins! Thanks so much for your sweet feedback. I would make sure to measure out the mashed bananas and not just use two bananas. That could make your batter super liquidy. The muffins are supposed to be moist but not super mushy inside (as in raw). I don’t have much experience with GF flour so I don’t know if that could also affect the batter.
I made them with Bob’s Red Mill One to One gluten free baking flour and they came out perfect!! Making another batch for this week!!
hello, this came out well, i added bittersweet chocolate pieces instead of choc chips. also added streusel topping. ????????
That’s so great! I love that you added streusel topping. I bet it was delicious 🙂
Would subbing avocado oil for the coconut oil work here?
I want to say it should be okay since avocado oil is very mild in taste but I haven’t experimented with it myself so I’m not 100% sure. But I would love to know how they turn out for you if you do end up making it with avocado oil. Good luck!
OMG. Look no further. Best muffins ever!!!! I want more of your recipes!
Thanks so much Jennifer!
Thank you for this wonderful recipe!
I used applesauce instead of bananas, and almond milk instead of milk. It turned a bit moistier than in your photos, but since I’m altitude baking, it was actually the kind f perfect that didn’t make it through cooling!
I tried again after Halloween, and topped them with shreaded coconut (unsweetened) and it’s just yummy!
Thanks so much Amber! So happy you loved the muffins with the ingredient swaps 🙂
Can I use applesauce instead of banana?
I can’t answer with certainty as I have not tried it with applesauce but if you do end up making them with applesauce, I would love to know how they turn out!
Hi, I was wondering if you thought it’d be ok to use canned pumpkin pie filling instead of the pumpkin puree…and then skipping the pumpkin pie spice? I know it wouldn’t be as healthy, but that way I could use what’s in the kitchen without going to the store after work. 🙂
I can’t really answer with certainty as I haven’t tried it with pumpkin filling but if it’s similar consistency as the puree and just sweetened then I don’t see why it wont work? Let me know if you do end up trying it!
We loved these muffins! Thank you! I appreciate baked goods that aren’t overly sweet. I enjoyed them as is… my boyfriend had them with a little honey drizzled on top!
Thank you so much Natalee! Glad to hear you enjoyed them. We love them not too sweet as well 🙂
These turned out fluffy, moist and delicious! This was the first time I baked muffins! My 3 year old loved them! The changes I made was substituting honey with organic jaggery 2tbsp in 1/4 cup water and clarified butter for coconut oil. Thank you for the recipe.
Thank you Nimitha! So glad you enjoyed these.
thanks for your tip on using jaggery, i tried it n came out well!
Can I use cashew milk?
I used almond milk and they turned out fantastically, so I’m sure you could 🙂
Thank you Kayli!
I can’t believe how great these are! I usually make a bunch of substitutions when I follow muffin recipes… and they don’t turn out well. I didn’t have to make any substitutions because you already did them… and I was so happy with them! Thank you!!
Thank you Jill! So happy you enjoyed them 🙂
Great recipes and the blog. I recommended your blog to several people at my work. 🙂
I’m looking for HEALTHY bran muffins recipe, I couldn’t find any on your blog. I LOVE bran muffins!
Most recipes have lots of sodium and sugar in it, spiking calories to 350 and beyond per one muffin with lots of carbs, quote from cookinglight.com: ” A random sampling of some coffee and restaurant chain bran muffins showed that many topped 350 calories apiece, and that’s before any butter or jam. The bran muffins at one popular chain bakery contain 600mg of sodium―roughly one-third of a day’s maximum.”
I want to challenge you to come up with a healthiest recipe for Bran Muffin! 🙂 It should taste good and not overloaded with sugar and sodium.
Do you think you can do it? I would like to have them for this Thanksgiving.
Thanks brother! I believe I’ve never has a bran muffin before but I like a good challenge 🙂 You inspired me.
Thanks for such an awesome recipe. I adapted it to make it vegan, but honestly couldn’t have made it taste so good without having your recipe as a guide. Super yummy and perfect for the fall!
Thanks Hayley! So happy you enjoyed them and I LOVE that you made them vegan.
I made them and they turned out great!! Also my recipe made 18, not 12. Perfect muffin for breakfast because there is no added sugar, I highly recommend! 🙂
That’s awesome Emily! So glad you enjoyed them.
I just made these with my 5 year old and they are delicious! Super moist and flavorful. I will definitely be making these again and again!
So glad you enjoyed them Lindsey! Thanks you for the feedback 🙂
Yum! Those look so good. I can’t believe it’s already fall!
I just made these and can’t wait to see if the kids love them – I already do!! Thanks for recipe!
Aww…thanks Supriya! Hope the kiddos enjoy them 🙂