Paleo Double Chocolate Pumpkin Muffins

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These Paleo Double Chocolate Pumpkin Muffins taste like a brownie. They don’t have a very noticeable pumpkin flavor, but adding pumpkin puree to the mix adds the perfect amount of moisture and a boost of nutrients to each bite.

double chocolate pumpkin muffins on a cooling rack

It never ceases to amaze me how flour-like a flourless muffin made with almond butter can be.

When paired with protein-rich eggs and low-glycemic coconut sugar, these healthier ingredients create a fluffy texture remarkably similar to a muffin made with white flour and sugar.

The only downside to these muffins is that they tend to be a little sticky– I imagine the baked muffins would stick to a greased pan, so definitely be sure to use cupcake liners. Preferably something like these silicone liners, which guarantee that nothing will stick. (And as an added bonus, they’re reusable– I’ve been using the same set for nearly 5 years now.)

I think these Paleo Double Chocolate Pumpkin Muffins are the perfect way to satisfy your sweet tooth without being overly sweet, especially since many of us might be coming off a sugar-high from Halloween treats. Because they’re loaded with plenty of fiber and protein, they’ll actually leave you feeling satiated, too!

Paleo Double Chocolate Pumpkin Muffins
Makes 12 muffins


1 cup creamy almond butter (store-bought or homemade)
1/2 cup pumpkin pumpkin puree
1/4 cup cocoa powder
2 whole eggs
1/2 teaspoon baking soda
1/4 teaspoon fine sea salt
1 teaspoon vanilla extract
1/2 cup coconut sugar
1/4 cup maple syrup
1/2 cup dark chocolate chips, plus more for topping


Preheat the oven to 350ºF and line a muffin tin with 12 baking cups. In a large bowl, stir together the almond butter, pumpkin, cocoa, eggs, baking soda, salt, vanilla, coconut sugar, and maple syrup. Once a smooth, thick batter is formed, fold in the dark chocolate chips.

Divide the batter among the 12 cups, then top each one with a sprinkling of extra dark chocolate chips, if desired. Bake at 350ºF until the muffins have risen, and the edges are firm to a gentle touch, about 20 minutes.

double chocolate pumpkin muffins on a cooling rack

Allow the muffins to cool completely before serving, and store any leftovers at room temperature, uncovered, for up to 4 days, or in the fridge for up to a week. I imagine these muffins would also freeze well, but there weren’t any left for me to test that theory on– we ate them all quickly!

double chocolate pumpkin muffin broken in half on a plate

Paleo Double Chocolate Pumpkin Muffins in silicone baking cups
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4.87 from 44 votes

Paleo Double Chocolate Pumpkin Muffins

A moist and fluffy chocolate muffin with a sneaky serving of pumpkin.
Course Breakfast
Cuisine American
Keyword Paleo Double Chocolate Pumpkin Muffins
Prep Time 5 minutes
Cook Time 20 minutes
Total Time 25 minutes
Servings 12
Calories 242kcal



  • Preheat the oven to 350ºF and line a muffin tin with 12 baking cups. In a large bowl, stir together the almond butter, pumpkin, cocoa, eggs, baking soda, salt, vanilla, coconut sugar, and maple syrup. Once a smooth, thick batter is formed, fold in the dark chocolate chips.
  • Divide the batter among the 12 cups, then top each one with a sprinkling of extra dark chocolate chips, if desired. Bake at 350ºF until the muffins have risen, and the edges are firm to a gentle touch, about 20 minutes.
  • Allow the muffins to cool completely before serving, and store any leftovers at room temperature, uncovered, for up to 4 days, or in the fridge for up to a week. I imagine these muffins would also freeze well, but there weren't any left for me to test that theory on-- we ate them all quickly!



Calories: 242kcal | Carbohydrates: 25g | Protein: 5g | Fat: 15g | Saturated Fat: 4g | Cholesterol: 32mg | Sodium: 156mg | Potassium: 84mg | Fiber: 4g | Sugar: 18g | Vitamin A: 900IU | Calcium: 70mg | Iron: 1.8mg
Per Serving: Calories: 242, Fat: 15g, Carbohydrates: 25g, Fiber: 4g, Protein: 5g

Note: If you don’t have maple syrup on hand, you’re welcome to replace it with an additional 1/4 cup of coconut sugar instead– the muffins will just be slightly less sweet. I think you could also use a different nut butter, if you prefer, just keep in mind that substitutions will change the flavor slightly.

Reader Feedback: What’s your favorite muffin flavor for this time of the year? 

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Lizette A.

Sounds yummy! Could you substitute honey for maple syrup. And, have you tried making in a bread pan instead of muffin cups?

    SHelley elmblad

    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!


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.

Laura ~ RYG

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!

    Megan Gilmore

    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
recipe 🙂

    Megan Gilmore

    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!

Lorie Evers

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.

out Theresa

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.


Hi Megan

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.
Thank you

    Megan Gilmore

    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! 🙂


What if u don’t have coconut sugar?

    Megan Gilmore

    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.

Erin L

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?

    Megan Gilmore

    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!

Erin l

I make these with tahini and they are deeeeelicious + nut free for school! Love them.

Chrysa Feggouli

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?

    Megan Gilmore

    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.

Julie Price

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.

Angie waters

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.

AnnIe Robison

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!

Lisa Avera

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!
Thank you!
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!

Dana Masden

Amazing. Favorite muffins. Nobody can ever believe that there is no flour in them.

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