Dark Chocolate Vegan Muffin Recipe

by Lindsay Cotter · 02/22/2021

This vegan muffin recipe uses dark chocolate, warm spices, and unrefined sugars. Rich in anti-inflammatory properties, these decadent, gluten free chocolate muffins are a treat for breakfast, snack, or dessert!

A hand holding a dark chocolate vegan muffin in white liner topped with dark chocolate chunks and sea salt flakes.

Y’all have been asking for recipes for vegan gluten free muffins for a LONG time. Because this is refined sugar free recipes month and we’re learning the facts about sugar, it’s the perfect opportunity to update my favorite recipe for chocolate muffins.

The original muffin recipe (published on April 27, 2016) was vegan and gluten free, but this update makes it refined sugar free as well. Healthier chocolaty goodness for the BIG win!
Many of the muffin recipes on the Web call for massive amounts of refined sugar, and to be honest, this is sad and sort of frustrating.

I mean, there is nothing wrong with enjoying something sweet for breakfast. I’m not one to turn down a plate of French Toast Pull Apart Bread or Sheet Pan Chocolate Protein Pancakes. My point is, overly sweet muffins are really just glorified cupcakes, aren’t they?

If you want a muffin that’s gluten free, vegan, and sweetened naturally, this recipe is exactly what you need! But if you truly want a muffin for dessert, it is easy to do! All you have to do is add a refined sugar free dessert sauce like vegan dulce de leche and your vegan chocolate muffins will become dessert!

vegan dulce de leche sauce dripping from spoon into jar of the sauce

Three dark chocolate vegan muffins stacked up on each other.

Mexican food, chocolate, and vegan gluten free muffins… they obviously go together. Plus, the fact that there’s this little holiday coming up that allows us to take our Mexican food adoration to a whole new level (ahem.. Cinco de Mayo!), we need to celebrate Mexican chocolate.

Health Benefits in this Chocolate Vegan Muffin Recipe

A little FYI: Authentic Mexican chocolate is a paste made from roasted, ground cacao nibs, refined sugar, and cinnamon. Other spices such as nutmeg and allspice are often used in Mexican chocolate as well, along with nuts, and even chili peppers.

Here in the states, the term Mexican chocolate is often used when referring to Mexican spices that we sometimes add to traditional milk or dark chocolate.

By combining the cacao nibs, Mexican spices, and unrefined sugars (coconut sugar and maple syrup), you’ve got yourself a much healthier treat, with health benefits!

Did you catch that? Mexican chocolate uses cacao nibs and has some pretty spectacular anti-inflammatory spices.

Cinnamon – My fave! Cinnamon can help to calm us, boost brain function, and it contains antibacterial properties that support healthy digestion.
Nutmeg– contains antioxidants and disease-preventing phytochemicals plus a hefty dose of Manganese which can help regulate the blood sugar.
Allspice– Contains an essential oil that aids in digestion. Plus it contains great anti-inflammatory properties.
Cacao – Known as the plant Theobroma cacao, cultivated for its seeds, known as cacao beans or cocoa beans. Super power antioxidants and helps promote healthy gut microbiome.
Chilies or chili powder– antioxidant and anti-inflammatory properties, and has shown to help reduce pain in muscles or joints due to inflammation.

Now, because adding white sugar to this vegan muffin recipe would probably undo all the health perks, I decided to naturally sweeten them with unrefined sugars instead.

Ingredients and Substitutions for Vegan Chocolate Muffins

measuring cups and prep bowls filled with ingredients for a dark chocolate vegan muffin recipe

Gluten free oat flour – You can buy this ready to use, or make your own by grinding gluten free oats in a food processor.

IMPORTANT: If you’re using homemade oat flour, you should weigh it after grinding, and then whisk/sift it before combining it with the other dry ingredients. This is important because each brand weighs differently per volume.

Spices – Ground cinnamon, nutmeg, and cayenne pepper. If you can’t have nightshades, you can omit the cayenne pepper.
Chocolate – You’ll need unsweetened cocoa powder and dark chocolate. If you happen to come across authentic Mexican chocolate made with unrefined sugar, use it! The best place to look for it is in a Mexican specialty store. Otherwise, choose an unsweetened extra dark chocolate, and be sure there are no hidden refined sugars!
Almond milk – Honestly, you can use any non-dairy milk you prefer. However, if you use coconut milk, be sure it’s brought to room temperature first. Otherwise, it can be difficult to incorporate with the other ingredients.
Sweeteners – Coconut sugar and maple syrup are my choices for this vegan muffin recipe. Other options are raw sugar (turbinado) or a plant-based sugar substitute like monk fruit.
Apple cider vinegar – There are some health benefits to using ACV, but white vinegar or lemon juice can be used instead.
Naturally refined coconut oil – You’ll be melting the oil, so if you prefer to melt plant-based butter, that will work as well.

one fluffy gluten free chocolate muffin topped with sea salt on white paper cupcake liner

How to Make Dark Chocolate Vegan Muffins – VIDEO

Dark Chocolate Vegan Muffins

Recipe notes

The reason I love this updated recipe so much is because these muffins are FLUFFY and MOIST. The previous recipe called for pumpkin puree, which is a heavy ingredient that ended up making the muffins very dense.

Longer rest times equals fluffier muffins! The longer the batter sits, the thicker it gets, due to the oat flour absorbing the liquid. If you let the batter sit for 10 minutes or so, the dark chocolate muffins will be extra moist, but don’t let it sit longer than that. Otherwise, your muffins won’t rise as much. Why? The baking soda/vinegar reaction will start to lose its effectiveness. It’s a balance game.

overhead photo: unbaked muffin batter in baking pan

overhead shot of chocolate gluten free muffins baked in muffin pan

You may need to grind the coconut sugar. If your coconut sugar or raw sugar is coarse, I recommend grinding it in a food processor so you can get a finer sugar texture.

A dark chocolate vegan muffin with white liner pulled back from edges, placed halfway into muffin tin well.

overhead image of a vegan chocolate muffin with bite taken out

Best way to store muffins

To keep them fresh for up to a week, be sure to store your chocolate muffins in an airtight container. It isn’t necessary to refrigerate them, but you can if you want to.

For longer storage (up to 3 months), place them in airtight freezer bags.

When you’re ready to serve them, either let them thaw at room temperature, or microwave the frozen muffins for a minute or so on high power.