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    Home » Recipes » Vegan Breakfast

    Gluten-Free Chocolate Muffins

    Modified: Mar 6, 2026 · by Puja Verma · This post may contain affiliate links · Leave a Comment

    Jump to Recipe Print Recipe

    Gluten-free chocolate muffins are rich, decadent, and indulgent! Bursting with cocoa and studded with vegan chocolate chips, they make the perfect breakfast companion or mid-day snack. Warm one up and enjoy its moist, fluffy interior, or pair it with your favorite vegan spread.

    Three stalked gluten-free chocolate muffins.

    Why you'll love this recipe

    • Allergen-friendly: Gluten-free chocolate muffins are perfect for those with gluten sensitivities or anyone looking for an allergy-friendly snack.
    • Easy to make: Even if you’re a baking newbie, this recipe is foolproof! Plus, it’s ready in less than an hour.
    • Wholesome ingredients: Packed with fiber from the oats and healthy fats from flaxseed and coconut oil, these gluten-free chocolate muffins are nutritious and delicious.

    Decadent gluten-free chocolate muffins

    Lately, my family has been on a total muffin kick! I’ve been baking batches of vegan blueberry muffins, vegan chocolate chip muffins, vegan strawberry muffins, and even vegan savory muffins.

    I wanted to add a double chocolate option to my repertoire, so I decided to whip up these gluten-free chocolate muffins! With a tender, moist crumb and bursts of chocolate chips in every bite, they perfectly blend health with indulgence.

    I love to serve them fresh out of the oven with a dab of vegan butter or a drizzle of almond or peanut butter. Enjoy them as a wholesome breakfast, afternoon snack, or healthy dessert!

    Are muffins vegan?

    Normally, muffins are not a vegan-friendly snack due to the dairy and egg products found in them. However, making a vegan option is easy! Here’s how I did it in this recipe:

    • Eggs: I used ground flaxseed combined with water as a vegan substitute for eggs, ensuring the muffins bind together and retain a moist texture.
    • Dairy: I replaced ingredients like milk and butter with dairy-free options like oat milk and coconut oil for an equally tender and delicious vegan treat.

    Ingredients & Substitutions

    Gluten-free chocolate muffin ingredients laid out individually with labels.
    • Rolled oats: Once blended, rolled oats provide a wholesome, gluten-free base in place of all-purpose flour. If you have oat flour, you can substitute the rolled oats with this to skip a step.
    • Baking powder: Gives the muffins their rise. Make sure to double-check that you have baking powder, not baking soda.
    • Cocoa powder: I use Dutch-processed cocoa to infuse the muffins with a deep chocolate flavor. You can replace it with cacao powder for a raw variant, but keep in mind that the flavor will vary.
    • Oat milk: Adds creaminess and a tender texture. Almond, coconut, cashew, or soy milk can also be used if you don’t have oat milk on hand.
    • Maple syrup: Used as a natural sweetener in the muffins. Agave, coconut nectar, or brown rice syrup also work as alternatives if you prefer.
    • Coconut oil: Provides moisture and structure. You can replace coconut oil with an equivalent amount of vegan butter if you’d like.
    • Vanilla extract: Enhances the flavor of these gluten-free chocolate muffins. Make sure to use pure vanilla extract over artificial vanilla for the best results.
    • Flaxseed: Acts as a vegan egg replacement, binding the muffin batter and adding moisture. Applesauce will also work. Use ¼ cup for every flax “egg.”
    • Vegan chocolate chips: For that extra chocolatey punch! Use any vegan-friendly chocolate chips or dark chocolate chips that don’t contain milk ingredients.
    • Apple cider vinegar: Helps make the muffins fluffy and tender. Regular white vinegar, lemon juice, or white wine vinegar will all work as well.

    How to make gluten-free chocolate muffins

    A mixing bowl with flax seeds combined with water.
    • Step 1: To make the flax egg, mix warm water and ground flaxseed. Let it sit and watch the magic happen. The flax mixture should thicken after about 15 minutes.
    A mixing bowl with wet ingredients in it.
    • Step 2: Add the rest of the wet ingredients to your flax egg, then mix it until it is well combined.
    An open blender cup with blended oat powder in it.
    • Step 3: Convert the rolled oats into oat flour with a quick blitz in your blender. Freshly-made oat flour gives a better texture, so use it if can!
    A mixing bowl with dry ingredients in it.
    • Step 4: Combine all the dry ingredients in a separate mixing bowl.
    A mixing bowl with chocolate batter in it.
    • Step 5: Gradually merge the dry ingredients into the wet mix, stirring as you go.
    A mixing bowl with chocolate batter and chocolate chips in it.
    • Step 6: Fold in the chocolate chips, and don’t forget the apple cider vinegar.
    A silicone muffin mold try filled with chocolate batter in each tin.
    • Step 7: Fill up silicone muffin molds or paper cup-lined muffin tins and bake your gluten-free chocolate muffins at 350F until fluffy.
    Gluten-free chocolate muffins on a cooling rack.

    Storage & Reheating

    For any leftover gluten-free chocolate muffins, keep the following storage instructions in mind:

    • Fridge: You can store your muffins in an airtight container for up to 3 days.
    • Freezer: Gluten-free chocolate muffins can be frozen for up to a month. Keep them in an airtight container or freezer-safe bag with parchment paper in between.
    • Reheating: To warm your muffins, heat them in a microwave for 20-30 seconds.

    Variations

    • Crunch: Add cacao nibs, chopped walnuts, or pecans for an extra crunchy texture.
    • Berry: Fold in fresh raspberries or blueberries for a berry-forward flavor.
    • Sugar: Before baking, sprinkle the muffin tops with raw sugar for a crunch.
    • Streusel: Make a quick streusel topping with oat flour, coconut oil or vegan butter, and cane sugar before baking the muffins.
    A bitten gluten-free chocolate muffin on a plate.

    Top tips

    • Wait on the flax egg: Ensure your flax egg has the right gel-like consistency. This is achieved by letting it sit for the full 15 minutes.
    • Check your batter: Your batter should be thick but pourable. Use the photos in this post as a guide.
    • Use quality chocolate: Opt for high-quality vegan chocolate chips for the richest flavor.
    • Don’t overmix: Gently fold the ingredients to keep the muffins light and airy. Overmixing will result in dense muffins.
    • Let them cool: Let your gluten-free chocolate muffins cool before digging in. This will prevent the muffins from falling apart.

    FAQ

    How do I know when my muffins are fully baked? 

    To ensure the muffins are fully baked, insert a toothpick into the center of one muffin. If it comes out fairly clean, they’re good to go!

    Can I use other gluten-free flour?

    This recipe is tested to be made with oat flour. Since gluten-free flours are all quite different, your results will vary if you try other options like coconut or almond flour.

    What do I do if my muffin batter is too thick?

    If your muffin batter is too thick, just adjust the mixture with a splash of milk until you reach the right consistency as shown in the photos.

    A bitten gluten-free chocolate muffin on a pate next to a cup of tea.

    More sweet recipes

    If you enjoyed this gluten-free chocolate muffins recipe, check out my collection of other vegan treats like these:

    • Vegan Flan: Rich, creamy, and indulgent flan made plant-based!
    • Flaxseed Pudding: A quick, healthy, and satisfying breakfast.
    • Vegan Mascarpone: Made from cashews, coconut cream, and vegan Greek yogurt.
    • Vegan Crème Brûlée: A crunchy, creamy, and ultra-satisfying dessert.
    Three gluten-free chocolate muffins stalked over each other.

    Gluten Free Chocolate Muffins

    5 from 2 votes
    Prep Time: 10 minutes mins
    Cook Time: 30 minutes mins
    Serving Size: 12 muffins
    Author Puja Verma
    Print Recipe Pin Recipe

    DESCRIPTION

    These gluten-free chocolate muffins are great for a wholesome breakfast, afternoon snack or healthy dessert. They are 100% vegan, packed with fiber and healthy fats. With a tender, moist crumb and bursts of chocolate chips in every bite, they perfectly blend health with indulgence. Serve them fresh out of the oven with a side of hot coffee or tea.

    INGREDIENTS
      

    Dry Ingredients

    • 2 ½ cups rolled oats
    • 2 teaspoon baking powder
    • 2 tablespoon cocoa powder

    Wet Ingredients

    • 1 ¼ cup oat milk lukewarm
    • 6 tablespoon maple syrup
    • 3 tablespoon coconut oil melted
    • 1 teaspoon vanilla extract

    Other

    • 2 tablespoon flaxseed (milled) ground
    • ¼ cup hot water
    • ¼ cup vegan chocolate chips mini
    • 1 tbsp apple cider vinegar

    METHOD
     

    • Preheat oven to 350℉.
    • To make the flax eggs - Combine warm water and flax seed ground in a medium size mixing bowl. Set aside for 15 minutes till it forms an egg-like consistency.
      Note: To warm up your water - Just microwave it for 30 seconds.
    • Then add all the wet ingredients to the flax egg (melted coconut oil, oat milk, maple syrup, vanilla extract). Mix all together till well combined.
      Note: To warm up your milk - Microwave it for 1 minute in then give it a quick stir.
    • Add rolled oats to a personal blender and blend till you have fine powdery flour. It measures to a little over 2 cups of oat flour after blending.
      Note: You can skip this step by using straight up oat flour.
    • Combine all the dry ingredients (oat flour, baking powder, cocoa powder) in a separate mixing bowl.
    • Slowly add the dry ingredients to the wet ingredients and mix well till it is all combined and comes together as a batter.
    • Fold in the chocolate chips. Then roughly mix in the apple cider vinegar.
    • Use a silicon muffin mold and evenly fill each muffin mold with the mixture. Bake for 30 minutes.
      Note: If not using a silicon muffin mold, then make sure to fill the tins with muffin/cupcake liners.
    • Remove the muffins from the oven and let them sit in the mold for 15 minutes. Allow them to cool off before removing them from the tins.

    NOTES

    • Wait on the flax egg: Ensure your flax egg has the right gel-like consistency. This is achieved by letting it sit for the full 10-15 minutes.
    • Check your batter: Your batter should be thick but pourable. Use the photos in this post as a guide.
    • Use quality chocolate: Opt for high-quality vegan chocolate chips for the richest flavor.
    • Don’t overmix: Gently fold the ingredients to keep the muffins light and airy. Overmixing will result in dense muffins.
    • Let them cool: Let your gluten-free chocolate muffins cool before digging in. This will prevent the muffins from falling apart.

    NUTRITION

    Calories: 1888kcal | Carbohydrates: 283g | Protein: 37g | Fat: 76g | Saturated Fat: 47g | Polyunsaturated Fat: 6g | Monounsaturated Fat: 9g | Sodium: 1037mg | Potassium: 1320mg | Fiber: 31g | Sugar: 96g | Calcium: 800mg | Iron: 16mg
    Course: Breakfast, Dessert, Snack
    Cuisine: American
    Keyword: gluten free chocolate chip muffins, gluten free chocolate muffins
    Tried this recipe?Let us know how it was!

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    5 from 2 votes (2 ratings without comment)

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    Puja from Green Heart Love

    I’m Puja! I love creating, developing & exploring vegan recipes made entirely from whole food & plant based ingredients.

    More about me →

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