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Home ❯ Recipes ❯ Vegan Snack Recipes

Healthy Chocolate Muffins

Lori standing in her kitchen.
Updated 12/06/2024 by Lori Rasmussen. This post may contain affiliate links.
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These healthier chocolate muffins are vegan, lightly sweetened, full of cocoa and chocolate chips, and both tender and satisfying thanks to whole-grain oat flour. You'll love how easy they are to make, with simple ingredients, and the pantry-friendly, secret ingredient replacing eggs and oil-pssst, it's canned pumpkin!

Dark chocolate muffins on a cutting board.

Adapted from my vegan pumpkin muffin recipe, these healthy vegan chocolate muffins are made with gluten-free oat flour and use pumpkin to replace oil and eggs.

But don't worry, you can't actually taste the pumpkin! It adds moisture and helps bind these naturally gluten-free muffins that would otherwise be a bit crumbly.

And of course, cocoa powder and chocolate chips bring all the chocolate vibes.

We love that these aren't a cloyingly sweet or heavy muffin. The fiber in the oat flour and fat from the almond butter make them satisfying yet light enough to enjoy for breakfast or an afternoon snack.

They're easy to make, too! All you need are 13 ingredients and 30 minutes to whip up a batch.

Jump to:
  • Ingredient Notes
  • How to Make Healthy Chocolate Muffins
  • Variations
  • How to Store
  • More Healthy Muffin Recipes
  • Recipe
  • 💬 Comments

Ingredient Notes

a labeled photo of the 14 ingredients needed to make vegan chocolate muffins.
  • Oat flour - you can buy oat flour online and in many stores, or make your own oat flour by blending rolled oats until they're the consistency of flour. Super easy!
  • Nut butter - I used raw almond butter but any other runny nut or seed butter you like is fine. Try Sunbutter for a nut-free option.
  • Canned pumpkin - our key, secret ingredient. This works as a binder and adds moisture to the oil-free batter.
  • Maple syrup - I can't recommend any substitutions. Maple syrup sweetens the muffins, adds flavor, and contributes moisture.
  • Cocoa - look for regular, unsweetened cocoa powder for the best flavor. Unlike Dutch process cocoa, it is naturally acidic and reacts with baking soda to help the muffins rise.
  • Coffee - hopefully you have some cold brew or strong brewed coffee on hand because they're great at enhancing the chocolate flavor. If not, a splash of good quality balsamic vinegar is nice, too.

See the recipe card below for amounts and full instructions.

How to Make Healthy Chocolate Muffins

a 3-photo collage showing the steps of making the batter and filling muffin tin.
  1. In a small bowl combine the wet ingredients. In a mixing bowl whisk together the dry ingredients.
  2. Pour wet into dry and stir to combine. Fold in the chocolate chips.
  3. Divide the batter among a standard 12-cup muffin pan. Add a few chocolate chips on top of each one. Bake for 19 to 21 minutes or until a toothpick inserted in the center comes out clean.

Cool in the pan for 10 minutes then transfer the muffins to a cooling rack.

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A muffin cut in half to show texture and chocolate chips inside.

Variations

  • Spiced - similar to this vegan chocolate zucchini bread, try the Mexican-chocolate inspired spices - cinnamon, chile powder, and cayenne. Or skip the chile and cayenne and pair cinnamon with ground ginger. Delicious!
  • With nuts- we always enjoy a little extra crunch in our muffins. Chopped walnuts and pecans are really good here.
  • Refined sugar-free - for a fully WFPB muffin (whole-food plant-based), instead of sugar-sweetened chocolate chips, use grain-sweetened carob or sugar-free chocolate. There are more varieties of sugar-free chocolate out there than ever!

How to Store

Store the chocolate muffins in an airtight container at room temperature for up to 2 days or refrigerated for up to 6 days.

The muffins freeze well, too. Make sure they are protected from air in a freezer-safe container. Thaw overnight in the refrigerator.

Related: if you enjoy healthier chocolate treats, don't miss these oil-free banana brownies!

More Healthy Muffin Recipes

  • Vegan banana blueberry muffins lined up on a cooling rack.
    Healthy Vegan Blueberry Banana Muffins
  • Vegan banana coffee cake muffins on a wire cooling rack.
    Banana Coffee Cake Muffins
  • close up of muffins lined up on a cooling rack with icing on top.
    Vegan Lemon Poppy Seed Muffins
  • Vegan pistachio muffins on a cooling rack.
    Vegan Pistachio Muffins

I hope you enjoy these healthy vegan chocolate muffins. If you try the recipe be sure to give it a star rating and comment below to let us know!

Recipe

close up of vegan chocolate muffin with other muffins in background.

Healthy Chocolate Muffins

Author: Lori Rasmussen, My Quiet Kitchen
These healthier chocolate muffins are vegan, lightly sweetened, full of cocoa and chocolate chips, and made with whole-grain oat flour. They're oil-free and delicious any time of day, from breakfast to dessert!
5 from 4 votes
Servings: 12 muffins
Prep:15 minutes mins
Cook:19 minutes mins
Total Time:34 minutes mins
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Equipment

  • standard muffin pan
(Keep screen awake)

Ingredients

Dry ingredients:

  • 2 cups oat flour - tap Metric to see weight in grams
  • ½ cup unsweetened cocoa powder
  • 1 teaspoon baking powder
  • ½ teaspoon baking soda
  • ½ teaspoon fine sea salt

Wet ingredients:

  • ¾ cup canned pumpkin puree - or sweet potato
  • ½ cup applesauce
  • ½ cup maple syrup plus 1 tablespoon
  • ⅓ cup unsweetened non-dairy milk - such as oat or soy
  • ¼ cup coconut sugar - or sub brown or cane sugar
  • ¼ cup runny almond butter - or other nut/seed butter
  • 2 tablespoons brewed coffee
  • 2 teaspoons vanilla extract
  • ½ cup non-dairy chocolate chips - plus more for tops of muffins

Instructions
 

  • Preheat oven to 375°F (190°C), and locate a non-stick muffin pan. Use paper liners if desired.
  • In a large mixing bowl whisk together all of the dry ingredients. In a smaller bowl stir together the wet ingredients. Pour wet into dry, and stir until a thick batter forms. Fold in the chocolate chips.
  • Divide the batter evenly among the muffin pan. Sprinkle a few more chocolate chips on top of each muffin.
  • Transfer the pan to the oven and immediately reduce the temperature to 355°F (180°C). Bake for 19 to 21 minutes or until a toothpick inserted in the center comes out clean. Let the muffins cool in the pan for 10 minutes, then transfer to a cooling rack.

Notes

Storage
Once muffins are completely cool, transfer to an airtight container. Store at room temperature for up to 3 days or refrigerated for up to 5 days. They can also be frozen. Thaw overnight in the refrigerator.

Estimated Nutrition (per serving)

Serving: 1muffinCalories: 218kcalCarbohydrates: 36gProtein: 5gFat: 7gCholesterol: 0mgSodium: 102mgFiber: 4gSugar: 20g

Nutrition information is an estimate and will vary depending on the exact amounts and specific products and ingredients used.

Did you make the recipe?Comment below to share your feedback!

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    Recipe Rating




  1. Julie says

    January 26, 2026 at 1:05 pm

    These were one of the BEST muffins I’ve ever made! Super moist and yummy! I used homemade applesauce and homemade cashew butter. I also used freshly made espresso instead of coffee. And topped the muffins with chopped pecans. Thanks Lori (:

    Reply
  2. Jean says

    May 17, 2024 at 8:27 pm

    Instead of canned pumpkin, could I use mashed bananas or alternatively extra apple sauce?

    Reply
    • Lori Rasmussen says

      May 18, 2024 at 11:00 am

      Hi Jean - Yes, I think mashed banana would be best.

      Reply
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I'm passionate about flavor and simplicity. I share vegan recipes with a focus on both!

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