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Moist and springy with a delightfully crunchy, sparkly sugar lid, these Gingerbread Muffins will add a bit of magic to any morning.

BEST Healthy Gingerbread Muffins made with chocolate, cocoa powder, whole wheat flour, coconut sugar, and Greek yogurt.

As my pantry, grocery cart for the last two weeks, and holiday baking list will attest, gingerbread is my absolute favorite holiday flavor.

From these Chocolate Ginger Molasses Cookies to these Gingerbread Apple Muffins, I’m a sucker for its warm spiciness and rich molasses notes.

Plus, since its sweetness is well balanced, I feel completely justified having it for breakfast, particularly in the form of these healthy chocolate gingerbread muffins.

If you are a gingerbread lover like me, then I can’t wait for you to try these fluffy gingerbread muffins! They’re going to be your new holiday favorite (or tied with these festive Cranberry Orange Muffins).

Healthy Chocolate Gingerbread Muffins made with coconut oil, Greek yogurt, and big chunks of dark chocolate in a muffin pan with a striped napkin

5 Star Review

“These are so delicious and tender! I’ve made these a few times now and they are one of our favorite holiday muffins!”

— Jennifer —

With their ultra-moist interiors (like these Coffee Cake Muffins), tops prime for picking with your fingers, and warming spices, these tender cinnamon and ginger muffins are exactly what I need to pull me out of bed (especially since Ben sneakily turns our house thermostat to 66 degrees after I fall asleep).

I also took the liberty of adding dark chocolate chunks (like in these Chocolate Muffins).

You can leave them out if you like, but once you’ve experienced a gingerbread muffin with pools of melty dark chocolate scattered throughout, it’s quite difficult to eat them any other way.

homemade gingerbread muffins filled with spices and chocolate and topped with sparkling sugar like a bakery muffin

How to Make Gingerbread Muffins

With warm winter spices, a kiss of chocolate, and robustly flavored molasses that keeps the muffins moist, gingerbread muffins are the perfect partner to your morning cup of coffee (or Crockpot Hot Chocolate).

The Ingredients

  • Flour. A blend of white whole wheat flour and all purpose flour keeps these gingerbread muffins wholesome enough for breakfast. (White whole wheat flour is also my stealthy healthy trick to these Healthy Blueberry Muffins.)
  • Greek Yogurt. Adds minimal fat, maximum moisture, and a healthy dose of protein.
  • Coconut Oil. For additional moisture and healthy fat. (I also use this healthy fat in these Coconut Flour Muffins.)
  • Coconut Sugar. An alternative sweetener made from the nectar of coconut palm tree blossoms, coconut sugar has a light caramel taste similar to brown sugar, and it can work as a direct replacement for white or brown sugar in many recipes.


Because coconut sugar is drier than brown sugar, I found that it works best to stir it in with the wet ingredients, let the mixture rest a few minutes, then proceed with the recipe as directed.

  • Molasses. The quintessential base for all-things gingerbread.
  • Spices. A blend of cinnamon, nutmeg, ginger, and cloves brings the gingerbread flavor of these muffins to life.
  • Cocoa Powder. To deepen the impact of the chocolate in every bite of these moist and decadent gingerbread chocolate muffins (and these Healthy Chocolate Muffins).
  • Dark Chocolate. If you haven’t tried combining chocolate and gingerbread before you’re missing out. There are luscious puddles of rich chocolate in every bite of these gingerbread muffins.
  • Sparkling Sugar. Also called Turbinado sugar, gives these muffins that perfect bakery-style top that will be the envy of your breakfast spread.
Ingredients for Healthy Chocolate Gingerbread Muffins made with coconut sugar

The Directions

  1. Melt the coconut oil in the microwave, then set it aside to cool to room temperature.
  2. Whisk together the yogurt, milk, coconut sugar, molasses, and egg. Then stir in the coconut oil.
  3. In a separate bowl, stir together the dry ingredients.
  4. Add the dry ingredients to the wet ingredients, stir gently, then fold in the chocolate.
  5. Divide the batter evenly into a greased or lined muffin pan then sprinkle the tops with sparkling sugar. 
  6. Bake the muffins until the tops are dry to the touch and a toothpick inserted in the center comes out clean. ENJOY!

Storage Tips

  • To Store. Place the gingerbread muffins in a paper towel-lined storage container and store at room temperature for up to 4 days. Don’t miss my How to Store Muffins for more tips.
  • To Freeze. Wrap muffins individually in plastic wrap and place them in an airtight freezer-safe storage container for up to 2 months.

Recommended Tools to Make Gingerbread Muffins

A fresh batch of chocolate gingerbread muffins in a muffin tin with one missing a bite

My favorite holiday flavor, in healthy breakfast muffin form! I know they’ll bring warmth to your mornings too.

Frequently Asked Questions

Can I Make Gingerbread Muffins Vegan?

Possibly. I have not made this recipe vegan before so it would be an experiment. I would suggest swapping for a non-dairy yogurt (such as coconut yogurt) in place of the Greek yogurt, substitute the egg for a flax egg, and ensure your chocolate is dairy free.

Can I Make Gingerbread Muffins Gluten Free?

I have not experimented with this recipe to make it gluten free. If you have a trusted 1-to-1 gluten free baking mix, you may swap it for the whole wheat and all-purpose fours. If you give this a try, I’d love to hear about your results.

Can I Use Blackstrap Molasses in Gingerbread Muffins?

No. I don’t personally recommend using blackstrap molasses in this recipe as it is too bitter and won’t compliment the other flavors in these muffins as well as regular molasses.

Gingerbread Muffins

5 from 12 votes
Moist and fluffy healthy gingerbread muffins with chocolate contain warm spices, whole wheat flour, and cocoa for a special indulgence.

Prep: 15 minutes
Cook: 16 minutes
Total: 31 minutes

Servings: 12 muffins


  • 1/4 cup coconut oil
  • 3/4 cup plain nonfat Greek yogurt at room temperature
  • 1/2 cup nonfat milk at room temperature
  • 1/2 cup coconut sugar or substitute light or dark brown sugar
  • 1/2 cup molasses not blackstrap
  • 1 large egg at room temperature
  • 1 cup plus 2 tablespoons white whole wheat flour
  • 1 cup all-purpose flour
  • 1/3 cup unsweetened cocoa powder sifted if clumpy
  • 1 1/2 teaspoons baking soda
  • 1 1/2 teaspoons ground ginger
  • 1 teaspoon ground cinnamon
  • 1/2 teaspoon kosher salt
  • 1/4 teaspoon ground cloves
  • 1/4 teaspoon ground nutmeg freshly grated if possible
  • 4 ounces chopped dark chocolate or 2/3 cup semisweet chocolate chips
  • sparkling (sanding) sugar for topping


  • Place a rack in the center of your oven, then preheat the oven to 375 degrees F. Lightly coat a muffin tin with nonstick cooking spray or line with paper liners. In a small bowl, melt the coconut oil in the microwave, then set aside to cool to room temperature.
  • In a large mixing bowl, whisk together the yogurt, milk, coconut sugar, molasses, and egg. Let rest for 5 minutes for the coconut sugar to dissolve slightly. If the mixture is not yet at room temperature, wait for a few additional minutes, then add the coconut oil. (If the wet ingredients are much colder than the coconut oil, the oil will resolidify and not incorporate properly.)
  • In a separate bowl, stir together the white whole wheat flour, all-purpose flour, cocoa powder, baking soda, ginger, cinnamon, salt, cloves, and nutmeg until evenly combined and no clumps remain.
  • Add all at once to the wet ingredients, then stir gently, just until combined. Fold in the chopped chocolate or chocolate chips.
  • Divide the batter evenly among the prepared muffin cups, then sprinkle the tops with sparkling sugar. 
  • Bake the muffins for 16 to 18 minutes, until the tops are dry to the touch and a toothpick inserted in the center comes out clean. Let cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.


  • TO STORE: Place the gingerbread muffins in a paper towel-lined storage container and store at room temperature for up to 4 days. Don’t miss my How to Store Muffins for more tips.
  • TO FREEZE. Wrap muffins individually in plastic wrap and place them in an airtight freezer-safe storage container for up to 2 months.


Serving: 1muffinCalories: 263kcalCarbohydrates: 41gProtein: 6gFat: 9gSaturated Fat: 6gCholesterol: 16mgFiber: 3gSugar: 23g

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Erin Clarke

Hi, I'm Erin Clarke, and I'm fearlessly dedicated to making healthy food that's affordable, easy-to-make, and best of all DELISH. I'm the author and recipe developer here at and of The Well Plated Cookbook. I adore both sweets and veggies, and I am on a mission to save you time and dishes. WELCOME!

Learn more about Erin

5 from 12 votes (2 ratings without comment)

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  1. These are lovely! A batch disappeared in less than a week! Thinking about baking them in my mini loaf pans next time…5 stars

    1. Bridget, I am so happy to hear that!! Thanks for trying the recipe and letting me know. I think these would be great in mini loaf pans too :)

  2. I’m back! :)
    Turns out these are not only wonderful muffins but also terrific mini loaves. A batch makes 3 mini loaves (5.5″x3″ pans, 1 1/3 cup batter each tin) which I bake at your given temperature for about 35 minutes. This recipe came at the perfect time for holiday baking and gift-giving. 

    ps. I also made mini loaves using your chocolate pumpkin loaf recipe (same tins, 1 1/4 – 1 1/3 cups batter per tin for about 30-35 minutes), which turned out brilliantly as well. 

    I admit, I’m starting to get a little holiday baking fatigue, but still can’t wait to see what recipes you have in store for us next! (Love muffins and loaves with yoghurt!) Thanks again, Erin! :)5 stars

    1. HI Bridget! I’m so, so happy that this recipe turned out for you this way (and the pumpkin bread too!) I have another yummy quick bread recipe coming up for Christmas that I hope you’ll love too. Stay tuned :) Thanks so much for taking time to leave your review!

    1. Hi Atoosa, I haven’t tried these muffins dairy free, so I can’t say for sure. If you have a non-dairy milk and yogurt that you’ve substituted before in other recipes and liked the result, you could experiment and see how it turns out here!

  3. I just made these and they are delicious! Kid approved too :). I only had blackstrap molasses so I used it but cut it with a little maple syrup too. Good gingerbread spice, which is what I like. Love your recipes and blog, thanks!5 stars

  4. These are delicious!  They’re great as muffins, but I think you could frost them and call them cupcakes as well.  The crumb is very light, moist and tender.  I used cappuccino Balkan yogurt instead of Greek, and subbed 1/3 cup chopped crystallized ginger for the dark chocolate.  The spices are well balanced and not too strong.  5 stars

    1. I’m so happy to hear that this recipe was a hit, Sadie! Thank you for taking the time to share this kind review!

  5. These are so delicious and tender! I’ve made these a few times now and they are one of our favorite holiday muffins!5 stars

  6. These are amazing! So moist and fluffy. Since we only have full fat dairy, that’s what I used. Everyone loves them, and I will definitely make these again. Thanks for the recipe.5 stars

  7. Hi Erin, Just made these muffins & they are awesome! Moist and flavorful. In fact I bake and cook your recipes all the time and they never disappoint. Please don’t ask me my favorite because they all are.😋. Thank You!5 stars

  8. Oh my, these are delectable! Some people are disappointed when a dark fudgy looking muffin turns out to be gingerbread not chocolate but these little dreams are the best of both worlds and everybody adores them! Just a note, I used what I had on hand: semisweet chocolate chips, avocado oil and white sparkling sugar for the top which made them reminiscent of chocolate crinkle cookies. Thanks, Erin, for introducing me to the gingerbread chocolate pairing. It’s INSPIRED5 stars