These Healthy Chocolate Muffins taste like a brownie, with a sneaky veggie hidden inside. There’s no flour or oil required, so they are naturally gluten-free, and kids love them!
Why You’ll Love Them
They taste amazing. This muffin recipe tastes like a cross between a chocolate cake and a brownie. They are ultra-satisfying when your sweet tooth strikes, and are loaded with fiber to help avoid any drastic blood sugar spikes.
They are nourishing. Made with almond butter and eggs, these muffins are a good source of protein, and taste like dessert. You’d never know that there’s pumpkin puree hidden inside! (It’s for texture, not flavor.)
They are gluten-free. Instead of using dry ingredients, like white whole wheat flour or oat flour, this recipe is flourless, which means it’s also gluten-free. The almond butter and eggs work together to create a fluffy texture you’ll love, with no oil required.
They are an easy option on-the-go. These healthy muffins make a delicious breakfast or snack, when you need something quick to grab.
Ingredients You’ll Need
This pumpkin puree in this recipe adds extra nutrients and moisture, without adding a noticeable flavor. If you don’t have canned pumpkin on hand, you could swap it for mashed ripe banana or unsweetened applesauce, but keep in mind that both of those options will change the rich chocolate flavor.
You could also use Greek yogurt as a substitute, if you don’t need a dairy-free recipe.
How to Make Healthy Chocolate Muffins
1. Mix the wet ingredients.
In a large mixing bowl, combine the almond butter, pumpkin puree, eggs, coconut sugar, maple syrup, cacao powder, vanilla extract, baking soda, and salt.
Mix well, until the batter looks smooth. Fold in the chocolate chips, if you want a double chocolate muffin.
Line a muffin tin with 12 liners, then use a 1/4 cup measure to scoop the batter into each spot. You should get 12 muffins from this recipe.
Sprinkle a few extra chocolate chips on top, if you’d like.
Bake in the oven at 350ºF for 25 minutes, or until the tops of the muffins rise and look dry on top. If the center of the muffin sinks significantly, that means they probably didn’t cook quite long enough.
You can also test the center of the muffin with a toothpick, if you prefer.
Let the muffins cool in the pan for 20 minutes, then transfer them to a wire rack to finish cooling completely.
Serve the muffins at room temperature, then store any leftovers in an airtight container in the fridge for up to a week.
Frequently Asked Questions
Yes, you can store the muffins in an airtight container in the freezer for up to 3 months. To thaw, place them in the fridge for up to 48 hours so they can soften again.
You can replace the maple syrup with honey, if you prefer, but the honey flavor will be slightly more noticeable. I don’t recommend replacing the granulated sugar with a liquid sweetener, or you might not achieve the same texture, but you can use another granulated sugar, if you need to.
If you grease the pan with cooking spray or coconut oil, the muffins will not release quite as nicely. (The muffin liners guarantee they’ll come of out the pan easily.) Without the liners, you’ll probably need to run a knife around the edges to help them release from the pan.
You can swap the cacao powder for cocoa powder, if that’s what you keep on hand, and you can also use peanut butter instead of almond butter, if you prefer. (The peanut butter creates a slightly drier texture.) If you want to try another veggie puree, you can toss raw zucchini in a blender to create a zucchini puree that could be used instead of the pumpkin.
You can add a teaspoon of espresso powder, if you keep it on hand, to emphasize the chocolate taste. For a less-sweet muffin, you can also cut back on the maple syrup, for a darker chocolate flavor.
Looking for more healthy muffin recipes? Try Blender Banana Oatmeal Muffins, Raspberry Chocolate Chip Almond Flour Muffins, or Chocolate Zucchini Muffins, for another variation.
Healthy Chocolate Muffins
- 1 cup creamy almond butter
- ½ cup pumpkin pumpkin puree
- 2 whole eggs
- ¼ cup maple syrup
- ½ cup coconut sugar
- ¼ cup cacao powder
- 1 teaspoon vanilla extract
- ½ teaspoon baking soda
- ¼ teaspoon fine sea salt
- ½ cup dark chocolate chips , plus more for topping
- Preheat the oven to 350ºF and line a muffin tin with 12 muffin liners. In a large bowl, stir together the almond butter, pumpkin puree, eggs, maple syrup, coconut sugar, cacao powder, vanilla extract, baking soda, and salt. Once the batter looks smooth, fold in the chocolate chips.
- Use a ¼ cup measure to divide the batter between the 12 prepared muffin cups. Sprinkle a few extra chocolate chips on top, if you like.
- Bake at 350ºF until the muffins have risen, and the center looks dry, about 25 minutes.
- Let the muffins to cool in the pan for 20 minutes, then transfer them to a wire rack to cool completely. You can serve them at room temperature, or store them in an airtight container in the fridge for up to a week.
- Nutrition information is for 1 of 12 muffins, including the chocolate chips. This information is automatically calculated, and is just an estimate, not a guarantee.
- See the full post above for substitution tips. You can use any other nut butter or fruit/veggie puree in this recipe for a similar texture, but the flavor will change depending on what you use.
- I haven’t had the chance to test a vegan version of this recipe yet, but I’ve had great success lately using psyllium “eggs” which seem to be more effective than flax eggs. To make 1 egg replacement, mix together 1 tablespoon whole psyllium husk with a 1/4 cup water until they gel together.
Update Note: This recipe used to be called “Paleo Double Chocolate Pumpkin Muffins,” but was updated in January 2023 with a new name and updated photos. I think the “pumpkin” in the title scared people off from trying them, and they are too delicious to miss! The recipe has not changed, but you can see the original version here.
If you try these healthy chocolate muffins, please leave a comment and star rating below letting me know how you like them.
Questions and Reviews
Sounds yummy! Could you substitute honey for maple syrup. And, have you tried making in a bread pan instead of muffin cups?
I bet using honey in place of maple syrup would work fine. I’m not sure how this would work baked in a pan, though. The edges may get dry by the time the middle set, but that’s just a guess.
I bake it in a pan all the time it makes a great bread!!! it needs to bake longer though. 45 minutes did it in my oven. I’d recommend checking it every few minutes after 45 if it’s not done!
I do this as well and make a snack cake. I add pecans or walnuts and white chocolate chips. It is delicious as this is one of my favorite recipes. You are right it takes a bit longer to cook, about 30ish minutes. I just checking after that at intervals of time to determine when it is done.
Do you think I could use flax eggs?
I would also be curios to know whether it would make any difference in replacing egg with flax or chia eggs.
Recently stumbled upon the chocolate & pumpkin combo and by was I pleasantly surprised!!!!! Struggling through the worst first trimester sickness (all day sickness) and trying to find foods that um, stay down? It’s odd because these would work. Perfect foods like veggies and chicken make me gag now!
Oh, congratulations on your pregnancy!!! I didn’t want any veggies during my first trimester, either. I think I lived off of bagels and pizza!! Both of which are totally unappealing to me now– anything I ate during my first trimester I hated by the time I reached my third trimester. Ha! Hope you feel better soon. 🙂
What is the nutritional value /information of this recipe? Trying to watch sugar intake along with glutton free. Would be nice if had that on your recipes.
I am sadly off nuts for the foreseeable future, but these looked so amazing that I decided to swap out the almond butter for sunflower seed butter. I used the Trader Joe’s brand, which although delicious, has a sweetener, and it made the muffins a little too sweet for my taste. They were nonetheless delicious — perfect texture and flavor — and I will definitely make them again. Next time I will plan to make my own seed butter, however, to control the sweet factor. A definite winner!
I made these muffins this morning in a mini muffin pan and they turned out great. I sprayed paper liners with coconut oil and baked for 15 min @ 350. Didn’t stick to the papers at all. They are delicious and so much like a traditional muffin. Kid and husband approved. Thank you for another great
I’m so glad to hear everyone enjoyed them! 🙂
Megan, these are amazing! I used cacao powder instead of cocoa. I made them as a desert for Thanksgiving and they were devoured by everyone. It was great to have a healthier alternative. Thanks so much for sharing!
These muffins are amazing. I love them. It’s like eating chocolate. Back when I used to eat box.cake there is that amazing texture well these muffins are even better.
Is here a replacement for the eggs? I am allergic to them sounds very good and I would like to try them
Would using homemade pumpkin puree work? Or would it throw of the flavor/texture? In the past, I’ve felt the difference between canned and fresh can be significant. If I did try it out, would you have any recommendations for adapting any ingredients? Thanks so much for your wonderful recipes!
Yes absolutely it will work, and this recipe tastes even better with homemade pumpkin puree. Actually there is a big difference between canned pumpkin and fresh pumpkin puree. I keep some frozen in the freezer in 1/2 portions just for the recipe throughout the year.
Goodness, these are a delicious treat! They’re so decadent, I’d consider them to be more like cupcakes than muffins. So good and easy!
Hello~ You might get a little chuckle out of this. I downloaded the My Fitness Pal app and when I got to the place to enter my birthdate, I realized that I had to hit each month starting with 1983 one month at a time till I got back to 1934! After nearly getting carpal tunnel, I finally got to 1942 and was pushing on thinking “I’m almost there!” only to have it revert back to 1983! My husband said they probably figured nobody that old was going to care about how many carbs in a pumpkin muffin. And by the way, they are excellent. I used walnuts instead of chocolate. He approved, too!
PS: Never could get to 1934. Do you have any ideas about carbs? I used Xyzitol…..only a couple of tablespoons if that much.
When you do your baking for deserts what rack level do you usually use?
As well, I am a big fan of your website which I discovered quite by accident. There is not a recipe that I have tried and not enjoyed. You have introduced me to a whole new way of cooking. I purchased your new book and love it.
Thanks, I’m glad you’re enjoying the new book! I always use the middle rack for baking. 🙂
I have now made these multiple times and this recipe has to be one of my favorites from Detoxinista. My only substitute is organic raw cacao powder and the finished product reminds me of a very decadent chocolate cake. For some reason, like with most Detoxinista recipes I had to bake a little bit longer then the recipe called for, but the texture is very cake/muffin like to me, yum! I have tried in both silicone muffin cups and in a 9×9 pan. Both came out great, but I definitely had to adjust for longer cooking time in the cake pan.
I don’t see myself getting tired of these anytime soon and when everybody at work brings cookies and donuts, I can have one of these instead!
Made these this weekend and they were SO SO good! My daughter (who can detect a “healthy” recipe a mile away) even liked them!…that’s saying a lot! Still so impressed how they turned out with no flour in them. Love all of your recipes! Everything I have made has turned out great! 🙂
I’m so glad to hear that! Glad you all enjoyed them! 🙂
What if u don’t have coconut sugar?
I only tested this recipe that way, so you’ll have to experiment if you want to use another sweetener. Sucanat might have similar results, or you could try a liquid natural sweetener making a more moist muffin.
These were awesome! I normally don’t comment but I had to for this one! My husband told me he would never have thought they were Paleo! Making again tonight!
This was most delicious muffin I have ever tasted ..I used cane sugar instead of coconut sugar …will be making them again soon.
These are delicious- like a mini brownie/cake! My hubby ate 4!! in one go. (Due to food allergies, he has limited “treat” options, so these were a major hit). Thank you!!!!
This recipe makes amazing brownies when put in a slice time and slightly u set so stays fudgy
I use tahini instead of nut butter because our school hasn’t banned tahini
Could applesauce be dubbed for the pumpkin? I have a few apples needing to be used up. These are delicious btw
These are incredibly delicious! Moist, fudgy consistency. They taste like they should be bad for you! I added peanut butter chips to mine instead of chocolate chips.
I made these with my 3 year old daughter today and they were phenomenal! So rich and moist. Better than traditional cupcakes with flour and white sugar. My daughter loved them and I can feel good about her eating them given the healthy ingredients. They will be our new go to when we are craving chocolate.
I made this before they came out perfect. I made them a second time and all the muffins sunk in? I don’t know what i did? Help?
Flourless muffins tend to sink if they don’t cook all the way through. It could just be that the second batch needed a few more minutes in the oven.
They didn’t look sunken in until they started to cool. Any tips to tell if baking is needed a bit longer since they appear puffed on the top? Thank you so much! These are incredible!
These muffins are AMAZING! I am 1 month into a dairy-free, grain-free, sugar-free lifestyle, and have been searching for simple, healthy, and yummy treats. The first bite was heavenly. (The rest of the bites were heavenly, too!) Thank you SO MUCH for this recipe!
I love these muffins and so does the rest of my family. Really delicious! Megan, I used to work with your mother-in law at the library and I miss chatting with her since she moved away. I was already familiar with your website before I met her, but she recommended I check out your book, which is wonderful. Thanks for the great recipes!!!
These are delicious! I used 1/2 cocoa and 1/2 cacoa and omitted the sugar. Plenty sweet! The batter tastes just like brownie batter. I licked the entire bowl clean!
Can this be made as a square sheet cake or a loaf? Any idea how that would change the name time or finished product? I made these muffins once with borrowed muffin tins and LOVED them. I don’t have those muffin tins and was hoping to make again for an event tomorrow!
I make these with tahini and they are deeeeelicious + nut free for school! Love them.
Can we use tahini instead of almond butter?
Moist and delicious. Best muffins I ever ate. Everyone loves them!
I really like this recipe but felt like they were over baked. I baked them for 12 min the second time and they seem perfect.
Is it possible to use agave nectar instead of the maple syrup? And is there some healthier alternative to coconut sugar?
These are hands-down the best Paleo muffins I have ever eaten! This is my go-to recipe to make and gift to my non-Paleo friends because everyone loves these!! I have done a lot of Paleo baking over the past 5 years and these are definitely the best!!
Is it possible to use dates instead of maplesyrup and coconut sugar? Like in your other pumpkin muffins that i absolute adore!!
Megan, could i replace the sugar an and syrup for dates like in your other pumpkin muffins? Thank you!!!
These were good, but they didn’t quite turnout the way yours did. I didn’t have eggs, so I substituted with flex eggs- two tbsp ground flax and six tbsp of water. It turned out too moist and sunk in the middle. I would think a flax egg should work here . . . Maybe do 1 tbsp of ground flax to two tbsp water? Aside from adding a little more cacao and nutmeg, I did the rest of the recipe to the letter. Thoughts? Also, my daughter is not big on nut butters. Any recommendations when you tested this recipe with using less nut butter? Maybe half nut butter, half tahini?
Flax eggs make a HUGE difference in flourless recipes. They usually work best as an egg substitute when making cookies (which don’t rise) or recipes with a gluten-based flour, which can bind without the eggs anyway. I’d recommend trying it with eggs next time if you can have them because it makes a HUGE difference! Feel free to experiment with the nut butter amount. I think tahini is much more bitter, so they won’t be as sweet if you use some of that.
These are so moist and a delicious breakfast treat! Super easy to make! Mine didn’t rise as much as the ones in the picture; they still tasted amazing! Such a protein packed muffin with the almond butter.
This is our all time favorite chocolate dessert and snack recipe. We use a little less sugar and maple syrup and add more (extra dark) chocolate chips. Not that the recipe is overly sweet – it’s not. It’s just that we’d rather have the decadence in the gooey chocolate chips, not the cake part. Don’t go cheap on the cocoa. We use Guittard Cocoa Rouge cocoa powder, which is very dark and rich. We also use Guittard extra dark (63% cacao) chips. If you can’t find Guittard, try Ghirardelli extra dark chips. We undercook a bit (remove from oven when just set) and when ready to eat we put in the microwave for 15 secs to melt the chocolate chips. It’s like chocolate lava cake.
These are really wonderful!! And they do freeze beautifully. I am making them for a second time now – didn’t have pumpkin but am using apple sauce. Thanks for another perfect recipe.
So, I made these for my daughter’s lunches, and then I tried them!!! I seriously can’t even describe how wildly delicious these are! Beautiful to look at, moist, great chocolate flavor…the list goes on! These may be my favorite muffin recipe of ALL time! I’m not sure how many of them will go into the lunch box, heehee!
Incredible!!! They tasted like a rich, fudgy brownie! I think next time I might bake in a pan and just call them brownies. So delicious!
I just want to say these are AMAZING! You have done it again! I have made 7 dozen in the last 3 days. My kids and grand kids LOVE these! They turn out perfect every time and look like I’m a professional cook! My daughter has requested me to make these and freeze them so she can just pop one out and stick it in her kids lunches for a healthy snack!
I’m so excited to have been able to witness and tried your recipes since before you had kids and how much you have grown in making amazing and wonderful food! Great job!
P.S. if I could rate these higher I would!
This is one of my favorite recipes. It is a forgiving recipe, you can sub in almost any nut butter. You can sub honey for the maple syrup. I use what ever I have on hand, mix and match, sometimes even mix nut butters if I only have 1/2 cup of one and 1/2 cup of another and it always turns out delicious. I can say though I roast my own pumpkins and freeze it, so much better than canned pumpkin and that does make a difference. I do not even eat cake or muffins anymore unless one of your recipes. These recipes are game changers for me. I could make a snack cake and in a day or two it would be gone, but with these muffins I eat one and I am satisfied. They are easy to make so I always have some in the freezer, and when I run out, I whip up another batch. Plus I love to back. My husband adores the muffins I make with your recipes from this one, which is my favorite, to the apple to banana one. He gets all the banana ones, I guess bananas are not my thing but he loves the muffins. And sometimes when he is home in the mornings, we have muffin dates where we have a muffin and coffee (sometimes for me herbal tea) together.
I would have never believed this recipe would work, but I was up to the challenge so I tried them because I like trying different things in the kitchen. Boy am I glad I did. I cannot thank you enough Meagan for coming up with your delicious muffin recipes.
Delicious! I was out of almond butter so I used peanut butter and they were fabulous. My husband – who’s usually suspect about my odd baking – has eaten 4 in the last 12 hours. I’ll definitely make these again. Thank you!
Hi, it’s the second time I make this recipe, and I’m disappointed with the result somehow. The taste is delicious, but the consistency is not. I get my kids to eat it with a spoon because it’s sticky. Maybe because so many wet ingredients? I don’t know. However, the other recipe I made which I find similar is the Flourless peanut butter banana muffins. It always turnes out perfect!….I wonder why do I get so different result.
These are INCREDIBLE!!!
Taste and texture is so super delicious, feels like I’m eating a fudge filled brownie/muffin.
Make them!!!! You’ll love ’em!
Amazing. Favorite muffins. Nobody can ever believe that there is no flour in them.