As my pantry, grocery cart for the last two weeks, and holiday baking list will attest, gingerbread is my absolute favorite holiday flavor. 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. Moist and springy with a delightfully crunchy, sparkly sugar lid, these holiday muffs will add a bit of magic to any morning.

BEST Healthy Gingerbread Muffins. Moist, easy bakery-style muffins with yummy chocolate and cocoa added for extra indulgence! Made with whole wheat flour, coconut sugar, and Greek yogurt, this is our favorite breakfast. Recipe includes vegan and gluten free options.

I knew I liked gingerbread, but it wasn’t until I took an honest evaluation of the impulse buys I made on my annual Trader Joe’s holiday product run that I realized just how deeply the two of us are involved.

I walked into the store for one item and walked out with gingerbread crisps, gingerbread cookies (which I ate with gingerbread ice cream I’d purchased earlier that week), gingerbread tea, chocolate-covered ginger…and about 17 other things I shared on my Instagram story. Oops.

These Chocolate Ginger Molasses Cookies are my favorite Christmas cookie of them all. These Gingerbread Apple Muffins are one of my most-loved breakfasts in the fall.

Sense a theme here? GINGERBREAD ♥

If you are a gingerbread lover like me, then I can’t wait for you to try these fluffy gingerbread muffins!

Healthy Chocolate Gingerbread Muffins made with coconut oil, Greek yogurt, and big chunks of dark chocolate. Every bite is filled with holiday spices!

With their ultra-moist interiors, 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 (if you haven’t tried chocolate and ginger together, you really must). 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.

This is the BEST gingerbread Muffin recipe. Moist and fluffy with lots of holiday spices and dark chocolate. Made with coconut oil and Greek yogurt, you'll never believe these are good for you too!

Fluffy gingerbread muffins filled with spices and chocolate! You'll never believe this recipe is healthy. Made with coconut oil, greek yogurt, and lots of spices.

Healthy Gingerbread Muffins for a Merry Morning

While gingerbread is typically thought of first as a dessert, I love it at breakfast too. The warm winter spices are the perfect company for my coffee, and the molasses heightens the flavor and makes the muffins even more moist.

To keep these gingerbread muffins wholesome enough for breakfast, I used whole wheat flour, Greek yogurt, coconut oil, and my new favorite healthy baking ingredient, Bob’s Red Mill Coconut Sugar. A wholesome 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.

Healthy Chocolate Gingerbread Muffins. Every bite is filled with chocolate!

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. I added just enough to these skinny gingerbread muffins to make them lightly sweet, while keeping them breakfast respectable.

I also wanted to make the gingerbread muffins healthy to leave wiggle room for two final flourishes: a shower of Bob’s Red Mill Sparkling Sugar and those hubba-hubba hunks of dark chocolate. The sugar crisps lightly while the gingerbread muffins bake, providing a yummy and addictive textural counterpoint to the moist muffin interior.

The dark chocolate? That’s for antioxidants and happiness (not necessarily in that order).

Gingerbread Muffins Recipe Variations

  • If you’d like to make vegan gingerbread muffins, I have a few suggestions in the recipe notes.
  • For gluten free gingerbread muffins, swap the flour called for in the recipe for a 1:1 GF baking blend like this one.

These muffins are also very freezer friendly. See my post for How to Store Muffins for details.

These gingerbread muffins are filled with chocolate and spices and they are good for your too! Looking for a healthy muffin recipe that doesn't taste healthy? This is it!

Recommended Tools to Make Gingerbread Muffins


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

The BEST Gingerbread Muffins made with Greek yogurt, coconut oil, and dark chocolate, Every bite is loaded with chocolate and spices. I can't believe these are healthy muffins!

Chocolate Gingerbread Muffins

5 from 12 votes
Moist and fluffy healthy gingerbread muffins made with warm spices, whole wheat flour, and chocolate for a special indulgence. Wholesome AND delicious!

Prep: 15 mins
Cook: 16 mins
Total: 40 mins

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
  • Bob's Red Mill Sparkling 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 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.


  • Store leftover muffins according to this guide for How to Store Muffins.
  • To make vegan: I have not yet tried this but this is my best estimate: use a nondairy yogurt (such as coconut yogurt) in place of the Greek yogurt, swap the egg for a flax egg, and ensure your chocolate is dairy free.


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

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I originally shared this post in partnership with Bob’s Red Mill in 2015. I am resharing it in 2018 because it is still one of my holiday favorites, and I know you’ll love it just as much this year too!

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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!

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  1. Oh, Erin, these sound so yummy! I, too, LOVE gingerbread anything! Thanks for another great recipe and hope you, Ben and Teddy are having a great holiday season! 

  2. 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

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