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Paleo Healthy Chocolate Muffins are a rich delicious snack, dessert or breakfast treat that’s actually nutrient-dense and easy to digest. Enjoy alongside some protein for a special fun meal.
This recipe is Paleo, Gluten-free, Low FODMAP and gives a soaked option for those who find it helps their digestion.
Jump to RecipeWhy are Paleo Chocolate Muffins healthy
Paleo Chocolate Muffins are as healthy as chocolate comes.
These muffins contain resistant starch and provide complex carbs for sustained energy!
The cocoa in the soaked version of Chocolate Muffins gives you more potassium and magnesium. (We’ll talk more about this.)
And these muffins also provide some protein and great fats. Served alongside protein, you’ve got yourself a super special weekend or weekday breakfast! Or throw these muffins into lunches, or serve them alongside soup.
How delicious are Paleo Healthy Chocolate Muffins
Paleo Chocolate Muffins are so delicious you may never need a piece of chocolate cake again. I’m not kidding.
With that crazy (easy to make) glaze on top and their middle texture and the oh-so-CHOCOLATE flavor, these muffins are as satisfying as you could hope for.
Fermentation of the batter
The fact that breads and quick breads can be fermented is tremendously magical and healthy. The purpose? Fermentation of breads makes the ingredients healthier.
Healthy is a vague word. When it comes to the fermentation of flours, healthy means that the nutrients become available and the anti-nutrients become gentler. Our bodies can easily digest and assimilate the nutrition in a fermented batter.
What’s happening? — We start out with a bowl full of dry ingredients: flour, cocoa, baking soda, sea salt, and in a separate bowl, wet ingredients: yogurt (or dairy-free yogurt) or another acid like apple cider vinegar, plus eggs, fat etc.
Phytic acid
When we combine the dry and wet ingredients and then let them sit … the acidity in the yogurt or apple cider vinegar changes the flour and cocoa! The acid neutralizes the phytic acid, oxalates and other anti-nutrients in the flours.
Phytic acid is the storage form of phosphorus in many plants. This compound is now called an anti-nutrient by many because it binds with minerals while it’s being digested in our guts, and actually robs our bodies of those minerals.
By neutralizing phytic acid, our bodies not only get the minerals in the other foods we’re eating, our bodies can also access the nutrition in the flours used, because that nutrition has become more bioavailable.
The short story is: Allowing our cassava and cocoa to soak overnight in a batter with yogurt (or dairy-free yogurt) allows us to get more nutrition from these flours and from the other ingredients in our meal.
Cocoa’s nutrition
When it comes to cocoa powder, this means we get more magnesium, potassium, sodium and calcium, more antioxidants and the increased potential for cardiovascular benefits — from a food touted to revive and nourish (source). As you may know, cocoa comes from a seed. And all seeds need to be “awakened” for us to access their nutrition. Read more about this here. Cacao beans undergo an initial fermentation shortly after their harvest. But fermenting the flour of the seeds/beans further enhances its nutrition and our body’s ability to assimilate that nutrition.
Personally, I have experienced the electrolyte balancing properties of cocoa. Cocoa is actually higher in potassium than other minerals so can help with renewed energy, fluid balance and cell integrity.
On the flip side, cocoa is high in copper, so I also don’t overdo chocolate.
Fermentation heightens flavor
Lastly, fermentation of cocoa also heightens its flavor. You’ll love the chocolate flavor of these muffins: The chocolate has been fermented twice, once shortly after harvest, as mentioned above, and a second time in your kitchen! You’ll notice the flavor and the perfume heightened …
The chocolate SMELL! This muffin batter smells amazing in the morning, after the overnight ferment!
I put the batter directly into the muffin pan the night before I bake, and set the pan in the oven, (so it can’t be raided by pests during the night).
In the morning, I pull the pan out of the oven to preheat it. And do you know what greets me? The almost heavenly aroma, SO RICH, of chocolate.
That perfume conveys the seeds’ release of flavor, the bloom you’ll soon taste! Watch out, too, while these muffins are baking! The fragrance of them permeates the whole house! You’ll always want to ferment your chocolate batters after you smell and taste the difference it makes.
When do the eggs get added
This batter, as mentioned above, ferments overnight at room temperature.
What about keeping the eggs in the batter at room temperature? This is a matter of personal preference. Here’s what to do: If you have farm eggs, just keep them at room temperature after collecting them. Then an overnight ferment is not an issue.
The conflict otherwise is that once eggs have been refrigerated, health departments don’t recommend keeping them at room temperature for more than four hours. Personally, I am not concerned about this. I have been fermenting batters for years and never once had an issue with food poisoning. The probiotics and acid in the yogurt (or ACV) help to keep any negative bacteria at bay. But if you are concerned, simply give your muffin batter the four hours it needs to ferment at room temperature, then bake; OR, then refrigerate until morning, and bake at that time. Your choice.
Muffins versus cupcakes
Lastly, what makes a chocolate muffin a muffin and not a cupcake? This is an important discussion, yes?
As young and lovely as I feel 🙂 , I am too old to mess around with cupcakes! I’ll keep making you cupcake recipes, don’t worry.
But for me, and my body, and my health history, I am completely content with the healthier the better, as long as it tastes good.
Muffins mean: soft, moist interior texture that doesn’t require butter or other condiments (unless you want to). Muffins mean less sweetener! Muffins mean: nutrient-dense. You add cocoa that’s been awakened (so its nutrients are bioavailable), and we have a slam-dunk-no-need-for-cupcakes-treat!
“Perfect texture,” is what my hubby says. So enjoy muffins for breakfast or anytime, because muffins this good satisfy the need to treat ourselves while also being good to our bodies.
What makes Paleo Chocolate Muffins triple chocolate
Inside the muffin batter is shaved chocolate (please see the recommended brands below the recipe, and be very careful what you choose to buy when it comes to chocolate); it’s optional and delicious.
On TOP of the muffins: the Glaze. I do NOT think the glaze should be optional. It’s incredible, and it’s easy to make!
And then, of course, the cocoa in the batter; that makes, “Triple”!
Paleo Healthy Chocolate Muffins {Soaked}
Equipment
- mixing bowl glass is ideal, not metal
- muffin pan
- oven
Ingredients
Chocolate Muffins
- 1 cup cassava flour Otto's preferred: see link below in Recipe Notes (Bob's is also okay. Do not use the other brands, as they are too high in starch from older cassava roots.)
- ½ cup butter or coconut oil, melted and cooled
- ½ cup cocoa powder Fair Trade only please
- ½ cup yogurt or dairy-free yogurt (or if you can't find dairy-free probiotic yogurt, + for Low FODMAP: use ½ cup minus 1 Tablespoon coconut milk + 1 Tablespoon apple cider vinegar)
- ⅓ cup maple syrup
- ¼ cup collagen see link and discount code below in Recipe Notes
- 3 eggs preferably room temperature
- 1 ounce unsweetened or bittersweet chocolate shaved
- 1 Tablespoon real vanilla extract
- ½ teaspoon baking soda sifted
- ¼ teaspoon sea salt
- flake salt for optional garnish (delicious!!); see link below in Recipe Notes
Chocolate Glaze
- ¼ cup cocoa butter melted -- to measure, place wafers (see link below in Recipe Notes) in ¼ cup measuring spoon so they are slightly heaping; then melt very gently (over low heat) in dry small skillet or saucepan; make sure all your cooking tools are dry, no water
- ¼ cup cocoa powder Fair Trade
- 4 drops stevia to taste (If you don't like stevia, it may be fine here to use powdered coconut sugar or powdered maple sugar, about 1 to 2 Tablespoons, to taste (Blend sugar in coffee grinder to powder.)
Instructions
(Preheat oven to 325℉ only if baking the muffins immediately.) Either way, line muffin cup pan with squares of torn parchment paper, or muffin cup liners. Set aside.
- Combine in bowl: eggs, yogurt, fat of choice, maple syrup and vanilla.
- In separate bowl, sift together cassava flour, cocoa powder, collagen, baking soda and sea salt. Add shaved chocolate.
- Add dry ingredients to wet ingredients, and use spatula to mix together thoroughly, without over-mixing.
- Fill lined muffin pan with batter. Place muffin pan in room temperature oven overnight (or for 4 hours) to ferment. (Muffins may also be baked immediately, if you don't wish to ferment the batter.)
If your muffins were stored in the oven for their overnight ferment, remove them now. Preheat oven to 325℉.
- Bake muffins until toothpick inserted into the center of one comes out clean, about 25 minutes for large muffins (start checking at about 18 minutes for smaller muffins). Allow muffins to cool slightly.
- Chill muffins 15 minutes in freezer to help glaze to set. Dip cooled muffins in glaze, or use spoon to ladle it over the tops, tilting muffins to the side so any extra runs off. As the glaze sets, sprinkle with flake salt. Allow to come to room temperature, and serve.
Chocolate Glaze
- In small bowl combine melted cocoa butter, cocoa powder and stevia (or powdered natural sugar). Whisk together until combined well. Set aside until muffins are chilled, before using. (Important Note: Make sure your bowl, whisk, spatula, melting pot [any and all tools used to make the chocolate glaze] are completely dry, no drops of water.)
Notes
Nutrition
Chocolate Bars to buy for this recipe and general use
We can affect some things in life. And buying a luxury item like chocolate is one area we should affect. I list below the chocolate bars I recommend.
Unfortunately, there aren’t more unsweetened Fair Trade ones. Did you know that many of the small chocolate companies that seem Fair Trade are actually owned by the egregious ones? It’s true: Avoid Dagoba and Scharffen Berger, to name two examples.
A lot of the Fair Trade bars have a bit of sugar in them (I really like this one if you can have 88% dark) or this one is good and uses honey. I actually love unsweetened chocolate bars in baked goods, and here’s a great option that’s truly Paleo (and still privately owned).
You can Pin this recipe here:
More Paleo Gluten-free chocolate recipes
- Tahini Brownies
- Best Paleo Chocolate Waffles
- Chocolate Ganache
- 4-ingredient Chocolate Ice Cream
- Ice Cream Mud Pie
- Cream Cheese Chocolate Cake (Primal)
Beverly says
I don’t see in the recipe where you use the shaved chocolate. Please let me know . These sound delicious, thanks.
Beverly
Megan says
Hi Beverly, it’s listed under Step 2. 🙂
Maria says
This is such a great information! What about if I can’t use eggs? Any suggestion? Tks
Megan says
I suggest you look into my many AIP recipes for egg-free. 🙂
Stacy says
Do you have any suggestions in place of cassava flour? I get terrible stomach aches with the cassava.
Megan says
Best to choose another recipe! I recommend my cookbook if you tolerate nuts and seeds well. Best wishes.
Deb says
These look amazing! Will be making them as soon as I get everything. You have a link to the cocoa nibs but I do not see where they are listed in the recipe. I am new to Paleo and trying to learn, what is the purpose of the collagen?
Megan says
Hi Deb, thanks for your comments and questions! I’m so excited for your Paleo journey!! I hope it’s wonderful and helpful for you! The nibs are just an option/alternative to use instead of shaved chocolate. But shaved chocolate is preferable. 🙂 Collagen has two purposes in this recipe: One, it adds protein so the muffins are extra safe for our blood sugar levels, and extra healthy. Two, it actually affects the texture by creating a more tender crumb. Blessings! 🙂
Kassia Batista says
Hi Megan, this looks delicious as always!!! I was wondering if honey would work in place of maple syrup and if I could reduce it to 1/4 cup? Or would the muffins be too bitter? Also how much honey would you recommend in the glaze in place of stevia? Would these make good mini muffins? Would they be good for young children as a treat or do they have too much caffeine? Sorry for all the questions!!
Megan says
Hi Kassia! Yes, you can sub honey in the muffin itself. I would NOT reduce the sweetener, because 1/3 cup is already very little for a muffin recipe, and it contributes to the moistness of the recipe. I would not use honey in the glaze unless you don’t mind it being wetter. It will still be good but it won’t stay as solid at room temperature. If you do this, you’ll use 2 tablespoons honey. (It will be a yummy frosting.) Yes, fine for mini muffins. Fine for kiddos if eaten with lots of protein as the main food, with muffin on the side in lesser quantity. Blessings! 🙂
Christina says
These look so rich and ahhhhhmazing!!! I’m loving all the chocolate and I’m really loving how you’ve made this healthier!!
Megan says
Thanks for your enthusiasm, Christina. It makes me happy. 🙂
Sharon says
These look wonderful. However I also have a sensitivity to eggs. This has been a tough one when it comes to baking and having things turn out right. Can these be made egg free and if so what would you recommend? Thanks so much.
Megan says
Hi Sharon, I’d type into my Search engine box “egg-free” and follow one of those recipes. I make a lot of egg-free recipes! 🙂 But it’s not ideal to try and adapt other recipes, because the recipe will turn out differently. Typically, when you do sub, you can use gelatin or chia seeds, as you probably know, to make gelatin or chia eggs in place of the eggs in the recipe. Let us know if you try this. 🙂
Katie Walsh Beck says
This sounds super interesting and like a great healthy option for a breakfast for my five kids 🙂
tessadomesticdiva says
These are right up my chocoholics alley…can;t wait to try them Megan! And the frosting!
Joni Gomes says
Hello chocolate, I love you! Muffins are always a good idea and I love this recipe!
Renee Kohley says
Ohhh man these look SO amazing Megan! My girls need a treat before we head back to school and they will think it is so special to get to have chocolate for breakfast!
Megan says
That’s really sweet, Renee. I can picture your girls’ faces; they are so appreciative it seems in general. Back to school! Agh, not so sure I’m ready! I’m loving these long, lazy days of summer!!
linda spiker says
Megan, these look positively scrumptious and decadent!
Megan says
Thanks Linda!!
whatggmaate says
There’s not one thing I don’t love about these muffins! That chocolate glaze on top is calling my name.
Megan says
Mine too, LOL. I need to make these again right away. Thank you! 🙂
Kassia Batista says
These were sooooooo delicious! They remind me of something from my childhood but I cant quite put my finger on it. I made them with the changes i asked about. I’m aready thinking these could be great as cupcakes for my birthday…maybe with a bit more honey and a whipped ganache instead of a glaze??? Anyways thanks for a delicious, super dark and decadent chocolate lovers muffin!
Megan says
Aw YAY!!! Thanks for sharing! It’s always SO good and comforting and happy to have a favorite chocolate recipe and to have a favorite muffin recipe, or both in one! 🙂 Your variation ideas sound low-risk/likely to be lovely!!
Kari says
All I can say is a big WOW! I had no idea you could ferment quick breads, but what a great idea, and the fact that they’re chocolate doesn’t hurt either!
Megan says
Haha, true. Thanks for your comment. I hope you get to make them and ferment batter. It’s super fun as well as being beneficial. 🙂
Raia Todd (@RaiasRecipes) says
Those muffins look absolutely amazing! I love trying new soaked recipes, so I’ll have to get my hands on some cassava flour and give these a try!
Megan says
Wonderful Raia!! Enjoy!
Karen @ Seasonal Cravings says
Wow, there is so much helpful info in this post. These look amazing and I’m new to the fermenting thing. I love all your tips for fair trade chocolate bc life cannot be lived without chocolate!
Megan says
Yes, thanks for appreciating the Fair Trade info!! Chocolate is so special. I’m so happy too that the info about fermenting resonates and is helpful. Thanks for your comments. Blessings!!
Lindsey Dietz says
Love everything about this! Thank you for being one of the few who recognizes and provides solutions for reducing phytic acid in cacao. And for raising awareness about Fair Trade and giving us ethical options! Mine are soaking now!
Megan says
Aw, wonderful Lindsey! Thanks for caring too about Fair Trade and phytic acid! All the care! 🙂 🙂
Carol Little R.H. @studiobotanica says
Thanks for the amazing recipe with cassava flour + all the important updated info re the chocolate companies. I am with you– in this day and age.. companies need to make a choice — a respectful choice.. and I will copy/paste your list to have on hand. We do have some local folks who I support.. I will grill them.. and then let u know about them — in case you are ok to add them.. to your list!
Our consumer dollars to add up to support the conscientious among us.. Appreciate your research!
Megan says
Thanks Carol!! 🙂
Emily @ Recipes to Nourish says
I cannot wait to make these soon. Gosh they are so perfect and I love that you’ve soaked them overnight for better health. I need to get my hands on that honey sweetened chocolate bar – how fun! Thank you for your thoughtful words about chocolate too – so important!
Megan says
Thank you love! So appreciate your words about the chocolate, and I hope you get your hands on one of those honey bars soon!! Also, wish I could send you the muffins!!
ChihYu Smith says
I can taste the yummy flavor from here! Gorgeous photos as well ! YUM!!
Megan says
Thank you ChihYu! 🙂
annelawton says
These muffins look so good! And thank you for sharing your list of fair trade chocolate companies.
Megan says
Thanks Anne! It means a lot that others out there care about Fair Trade. Much love and hope you get to make the muffins! 🙂
Lea says
So the info on chocolate is very good. Can you explain why we can’t trust the labeling for instance from this page? I don’t want I have anything to do with slave Labour, much less child slavery! So help me understand how to find trustworthy chocolate when at the local stores.
https://www.greenamerica.org/end-child-labor-cocoa/chocolate-scorecard
Megan says
Hi Lea, the site you link to seems fine, but I’m not sure it’s as accurate as the information I link to. For example, Hershey’s has pledged in the past to stop their child labor (by 2012 at one point), but they do not follow through. We’ll see in 2020 what they really do. The site you link to is very brief in their explanations. The sites I link to are more thorough; that’s all. In any case, the info I link to is a great guide for what to buy that is truly fair trade. All the links in this post should guide you for what to get at the market. I provide several companies from whom it’s safe to buy.
Jana says
I made these a couple days ago and they are so amazing. I made them non-dairy. This was my first time using liquid Stevia. I loved the bitterness of the frosting (I used 6 drops of Stevia). My frosting was a bit runny, not sure why, but still delicious. Thanks you for sharing….These are my new favorite chocolate item and will be a healthy substitute for the sugar filled dark chocolate bars I normally eat.
Megan says
Yay, terrific!! So happy to hear this! That’s how I feel about them too. I agree about the bitter glaze! 🙂 So … did you freeze the muffins briefly first so the glaze would set? It should be runny when it goes on, but then it sets because of the cold hitting the cocoa butter. Thanks for coming back to comment; it’s always great to hear feedback! 🙂
Jana says
I did freeze them, but I may not have let them cool long enough before freezing them. I will try again….for now, I am enjoying the muffins….. as I froze the rest of the batch so I could eat them one at a time when I want a chocolate treat. I re-heat in the toaster oven 🙂 Thanks again….I really love these!!!
Megan says
You’re welcome and so glad Jana!! 🙂
Daniela says
These muffins look insanely delicious! I really love that you included fair trade chocolate companies! These are in a league of their own!
Megan says
Ah, so true, thanks Daniela!!
Jen says
Do you think I could use kefir instead of the yogurt?
Megan says
Hi Jen, definitely!! 🙂 Enjoy! 🙂
Dorothy says
I made these recently, and it was a special treat to have them for breakfast. 🙂 I think it made eleven, so I guess mine were small. I used carob in the glaze and I suppose it could be used in place of cocoa in the muffins too? It looks like the cocoa powder you linked to isn’t available right now, but others would be. I’m glad to be more aware of the ethics of the companies that make chocolate.
Megan says
Great, Dorothy, I love this recipe, so am happy to know you enjoyed it as well. Yes, you can sub carob for the cocoa in the muffins. Thanks for letting me know I need to update that link! Yes, and thanks for your thoughtfulness about the chocolate companies. ❤