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Home › Recipes › By Type › Breakfasts
★★★★★49 Comments

Dark Chocolate Vegan Muffin Recipe

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by Lindsay Cotter Posted: February 22, 2021

Dairy-FreeEgg-FreeGluten-FreeNightshade-FreeNut-FreeVegan
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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.


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.

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

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!

dark chocolate shavings

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

  • Gluten free oat flour– You can buy this ready to use, or make your own by grinding gluten free oats in a food processor.
measuring cups and prep bowls filled with ingredients for a dark chocolate vegan muffin recipe

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.

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.

Print
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woman's hand holding a Mexican chocolate vegan muffin

Dark Chocolate Vegan Muffin Recipe


★★★★★

5 from 5 reviews

  • Author: Lindsay Cotter
  • Total Time: 29 minutes
  • Yield: 10 muffins 1x
  • Diet: Vegan
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Ingredients

Scale
  • 1 ¾ cup oat flour 195g * see notes
  • 1 teaspoon baking soda
  • ½ teaspoon kosher salt
  • ⅓ cup coconut palm sugar or cup-for-cup sugar substitute (see notes)
  • ½ cup unsweetened cocoa powder
  • 2 teaspoons ground cinnamon 
  • ⅛ teaspoon ground nutmeg
  • 1 cup almond or coconut milk, at room temperature
  • ¼ cup maple syrup
  • 1 teaspoon Mexican vanilla or pure vanilla extract
  • 2 ounces (¼ cup) naturally refined coconut oil, melted
  • ½ tablespoon apple cider vinegar or lemon juice
  • ½ cup dark chocolate chips
  • dark chocolate shavings and sea salt, to top. Or see notes for optional topping.

Instructions

  1. Preheat oven to 350°F. Line or grease a 12-cup muffin pan and set aside.
  2. In a large bowl, sift together the dry ingredients: oat flour, cocoa powder, baking soda and salt. Add the sugar and spices and mix to combine. Set aside.
  3. In a separate bowl, combine milk, maple syrup and vanilla extract. Stir together, then add to dry ingredients, gently stirring to combine. Add the oil and vinegar and gently mix again. Don’t over mix. Fold in chocolate chips or chopped dark chocolate.
  4. Spoon batter into greased or lined muffin tins, about  ¾ full.
  5. Transfer pan to preheated oven for 18-20 minutes (rotating halfway), or until a toothpick inserted into the center comes out clean or with a few moist crumbs. Baking times vary depending on your oven, so be sure to check progress around 15 minutes. 
  6. Remove pan from oven and let muffins cool in the pan on a cooling rack.
  7. Add toppings of choice (see notes)

Notes

  • If using homemade oat flour (grinding oats), be sure to weigh it after grinding and then whisk/sift before combining it with the dry ingredients. Be sure to weigh the oat flour because each brand weighs differently per volume.
  • 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 result will be a more moist muffin, but I would not let it sit longer than that or your muffins won’t rise as much. Why? The baking soda/vinegar reaction will start to lose its effectiveness. It’s a balance game.
  • 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.
  • Enjoy muffins as is, or top with dark chocolate shavings and sea salt, or vegan dulce de leche sauce.

This recipe was originally published on April 27, 2016. The recipe was re-tested and a video was added for republishing on February 22, 2021.

  • Prep Time: 10 min
  • Cook Time: 19 min
  • Category: snacks
  • Method: oven
  • Cuisine: American

Nutrition

  • Serving Size:
  • Calories: 213
  • Sugar: 13.5 g
  • Sodium: 217.1 mg
  • Fat: 9.8 g
  • Saturated Fat: 6.2 g
  • Carbohydrates: 29.4 g
  • Fiber: 3.2 g
  • Protein: 3.9 g
  • Cholesterol: 0.3 mg

Keywords: vegan muffin recipe, dark chocolate, vegan chocolate muffins, gluten free, dairy free

We have a new cookbook!

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Now, TELL ME…
Do you like to make muffin recipes to serve for breakfast, healthy snacks, or desserts. Or maybe, all of the above?

Enjoy your dark chocolate goodness!

LC

This recipe was originally published on April 27, 2016. The recipe was re-tested and a video was added for republishing on February 22, 2021.

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Categories: Breakfasts, Dairy-Free, Desserts, Egg-Free, Gluten-Free, Has Video, Nightshade-Free, Nut-Free, Oven, Snacks and Appetizers, Vegan, Vegetarian Tags: chocolate, kid friendly

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Lindsay Cotter of Cotter Crunch

About Lindsay

Hi, y’all, I’m Lindsay Cotter, a Nutrition Specialist with a focus on Gluten-Free eating. I love creating delicious nourishing food that anyone can enjoy.

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  1. Rebecca (Becky ) Nance

    02/22/2023 at 12:13 PM

    can you use regular oats ( quick cooking or old fashioned ) to make your own oat flour? I can’t wait to try this recipe

    Reply
    • Avatar photoSammi (Cotter Crunch Test Kitchen)

      02/22/2023 at 2:06 PM

      Hi Becky! Great question. Yes, you can use quick cooking or old fashioned oats to make oat flour. We have a whole post dedicated to making your own oat flour if you’re interested: https://www.cottercrunch.com/how-to-make-oat-flour/ Happy baking!

      Reply
  2. Denise

    02/07/2023 at 7:59 AM

    Any subs for oat flour? My hubby can’t tolerate it. Thank you!

    Reply
    • Avatar photoLindsay Cotter

      02/07/2023 at 9:52 AM

      What type of flour do you have on hand? A GF all purpose flour might work. Or quinoa flour.

      Reply
  3. Toni

    02/26/2021 at 7:21 AM

    These muffins are so good!! Glad they are healthy cause I ate more than two!!

    ★★★★★

    Reply
    • Avatar photoLindsay Cotter

      02/27/2021 at 5:16 PM

      Haha, I completely agree!

      Reply
  4. Renee Thiegpin

    02/24/2021 at 12:24 PM

    I am in love with the flavors in the muffins! All of my kids loved them, thank you!

    ★★★★★

    Reply
  5. wilhelmina

    02/24/2021 at 11:26 AM

    These muffins are incredible! They taste like such a treat, I had a hard time convincing my husband that they were actually healthy!

    ★★★★★

    Reply
    • Avatar photoLindsay Cotter

      02/27/2021 at 5:18 PM

      I think that’s what I love the most about the recipe too!

      Reply
  6. Toni

    02/24/2021 at 7:19 AM

    This is such an amazingly healthy muffin!! It tastes really good, too!

    ★★★★★

    Reply
  7. Karen Schott

    02/23/2021 at 12:09 PM

    Holy cow, these are so incredible. I was tempted to hide some from my kids 🙂

    ★★★★★

    Reply
  8. Cassie

    05/08/2016 at 3:14 PM

    Mexican hot chocolate is so much better than the normal one! Parisian hot chocolate is delicious too. I love all of the spices that goes into Mexican hot chocolate–these muffins look phenomenal and so deliciously moist inside!

    Reply
    • Cotter Crunch

      05/08/2016 at 9:13 PM

      Ohhh i gotta try!

      Reply
  9. Meghan@CleanEatsFastFeets

    04/30/2016 at 5:04 PM

    Chocolate for breakfast on repeat. I like the sound of that.

    Reply
  10. Jenny B

    04/30/2016 at 12:36 PM

    Your muffins look delicious but the recipe says gluten free – not Paleo. Is there a way to make them Paleo? I save and sometimes use many of your Paleo recipes. Thanks so much.

    Reply
    • Cotter Crunch

      04/30/2016 at 12:47 PM

      sure! can you have eggs?

      Reply
  11. Katie

    04/28/2016 at 6:39 PM

    I HAVEN”T FORGOTTEN ABOUT YOU! I promise I still read your posts daily!! These muffins look a—amazing! Totally making soon!

    Reply
    • Cotter Crunch

      04/28/2016 at 7:31 PM

      And I haven’t forgotten you! I hope you are well

      Reply
  12. Kristy @ Southern In Law

    04/28/2016 at 3:46 PM

    There is so much goodness going on in these little muffins! Yuuuuuuuuuuuummmmmmmm!

    Chocolate is always a winner with me but Mexican Chocolate is just a whole new level of deliciousness 😉

    Reply
    • Cotter Crunch

      04/28/2016 at 6:18 PM

      You know it!

      Reply
  13. Natasha @ Salt and Lavender

    04/28/2016 at 11:07 AM

    These look really tasty and I just love your photos!! Pinning 🙂

    Reply
    • Cotter Crunch

      04/28/2016 at 6:18 PM

      thank you friend!

      Reply
  14. Amanda @ .running with spoons.

    04/27/2016 at 8:42 PM

    I don’t think I’ve ever tried Mexican chocolate, but I did try chocolate with a little spice in it… which my wimpy taste buds couldn’t even handle 😆 I’ve heard that anything sweet is supposed to help with a burning tongue, though, so I’ll take a shot glass of dulce de leech sauce please 😀

    Reply
    • Cotter Crunch

      04/27/2016 at 9:27 PM

      OMG you must try! it’s not spicy. Promise!

      Reply
  15. Lauren @ The Bikini Experiment

    04/27/2016 at 7:03 PM

    I have not tried Mexican chocolate but it definitely on my radar. The muffins look fabulous. Healthy and yummy. Thanks for the recipe.

    Reply
    • Cotter Crunch

      04/27/2016 at 9:28 PM

      yea! thanks Lauren. Let me know if you try it.

      Reply
  16. Jody - Fit at 58

    04/27/2016 at 6:11 PM

    Yes Yes Yes!!!! Love all those spices too!!!!!!!!!!!!!!!

    Reply
    • Cotter Crunch

      04/27/2016 at 9:28 PM

      And i love you! <3

      Reply
      • Jody - Fit at 58

        04/28/2016 at 2:07 PM

        xoxoxo

        Reply
  17. rachel @ Athletic avocado

    04/27/2016 at 4:18 PM

    The fact that these are healthy and have a dulce de leech sauce too makes me want to throw my hands in the the air like I just don’t care haha!

    Reply
    • Cotter Crunch

      04/27/2016 at 9:27 PM

      yea! that’s the way to do it! haha

      Reply
  18. Erin @ Erin's Inside Job

    04/27/2016 at 10:27 AM

    These look delicious. I need some more chocolate in my life.

    Reply
    • Cotter Crunch

      04/27/2016 at 1:20 PM

      I can concur

      Reply
  19. Laura @ Sprint 2 the Table

    04/27/2016 at 10:27 AM

    I just don’t care! That’s classic.

    Those California figs are a sign. Head west. I need some adrenals support for this move – I know you have all the secrets.

    P.S. Who knew about the allspice?!

    Reply
  20. Shashi @ RunninSrilankan

    04/27/2016 at 10:19 AM

    Girlfriend, I have an idea – how about you eat that one muffin you are holding and send me the rest? Gosh darn it – you made these super healthy and seeing I have 0 self control when chocolate is in healthy form – I’ll take ’em ALL! xx

    Reply
  21. Blair

    04/27/2016 at 9:47 AM

    Chocolate + Spices + Muffins = a bite of breakfast (or snack) heaven!!!

    Reply
  22. Lucie@FitSwissChick

    04/27/2016 at 8:51 AM

    I am not sure if I can cheat on Swiss chocolate with Mexican chocolate….but yes, it is delicious, I tried it when I travelled there.
    And Dulce de Leche?! Oh sooooo gooood.

    Reply
    • Cotter Crunch

      04/27/2016 at 2:04 PM

      Oh yes, swiss chocolate and mexican chocolate need to have a baby. 😉 p.s miss you!

      Reply
  23. Sarah

    04/27/2016 at 8:11 AM

    Hello yum! Does this recipe yield a dozen? I was unable to find how many servings it made.

    Reply
    • Cotter Crunch

      04/27/2016 at 8:40 AM

      oh whoops! typo in my recipe. thanks for catching it. So if you fill cups 2/3rds full they make 12. If you fill 3/4 full they make 10. Hope that helps!

      Reply
  24. Lauren | Wicked Spatula

    04/27/2016 at 7:18 AM

    YASSS!! I can NOT wait until Friday for that dulce de leche recipe!! I’m loving that you sweetened them with figs too!

    Reply
  25. Annmarie

    04/27/2016 at 7:18 AM

    I have never had Mexican Chocolate but I guess that needs to change 😉

    Reply
  26. Rebecca @ Strength and Sunshine

    04/27/2016 at 6:53 AM

    I still haven’t spiked any chocolate treats with the SPICE! I should probably get to it!

    Reply
  27. Alexa [fooduzzi.com]

    04/27/2016 at 6:45 AM

    I LOVE this!! Literally anything with figs is my favorite 😉 So exciting about this recipe – pinned for later!

    Reply
  28. Megan @ Skinny Fitalicious

    04/27/2016 at 6:12 AM

    Mexican chocolate is the best! It’s one of the things I miss about working in Mexico. Now these I must try. Waving my hands like I just don’t care right now lol!

    Reply
    • Cotter Crunch

      04/27/2016 at 7:23 AM

      haha why i love you so!

      Reply
  29. Susie @ Suzlyfe

    04/27/2016 at 5:17 AM

    YAS. I love spicy Mexican chocolate. Really, I love most things about Mexico. I need a margarita.

    Reply
  30. Michele @ paleorunningmomma

    04/27/2016 at 5:05 AM

    Need these! Anytime chocolate gets a healthy twist I’m on board – and now I’m craving spicy Mexican chocolate. On another note you’re reminding me I’m really curious to try out a vegan muffin!

    Reply
    • Cotter Crunch

      04/27/2016 at 7:20 AM

      making vegan muffins with paleo flour is tricky but doable! I used bobs redmills 1:1 here so I could get more volume with the starch and acid. So they are not paleo but they are so fluffy and moist! You gotta try!

      Reply

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Lindsay Cotter of Cotter Crunch

About Lindsay

Hi, y’all, I’m Lindsay Cotter, a Nutrition Specialist with a focus on Gluten-Free eating. I love creating delicious nourishing food that anyone can enjoy.

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titled image (and shown) dark chocolate vegan muffin recipe