Chocolate Gingerbread Muffins

If classic seasonal flavors were a middle school gym class, poor gingerbread would be the kid who always gets picked last.

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!

I noticed gingerbread’s plight while perusing the holiday aisle at Target. In addition to the shiny red and green ribbons, twinkly lights, and glittery snowflakes, Target has a dangerously wonderful array of special seasonal treats. While peppermint and chocolate and even some stray pumpkin were all well represented, the gingerbread options were much harder to locate.

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

Yes, peppermint and sugar cookies might be the holiday gym team captains, but this year, I motion that gingerbread be the flavor we pick first. With its unabashed intensity of spice, depth of molasses, and warming presence, gingerbread is exactly the company I want to keep on a chilly evening or, in the case of today’s recipe for Chocolate Gingerbread Muffins, a crisp morning beside my cup of coffee.

With their ultra moist interior, fluffy top prime for picking with your fingers, and pools of melty dark chocolate within, these tender gingerbread muffins are exactly what I need to pull me out of bed, when our house thermostat is set to 65 degrees. (I wait for Ben to leave for work before I crank it up to a roaring 68.)

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.

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, 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 a dryer 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 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 hunks of dark chocolate. The sugar crisps lightly while the gingerbread muffins bake, providing a yummy and addictive texture counterpoint to the moist muffin interior.

The chunks of dark chocolate? Those are for antioxidants and happiness (not necessarily in that order).

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!

This Thanksgiving week, if you are craving a little healthy decadence in between all of the, well, decadence, treat yourself and your family to a big batch of these healthy Chocolate Gingerbread Muffins. Everyone (including you!) will be thankful.

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Chocolate Gingerbread Muffins

Soft and fluffy healthy gingerbread muffins made with coconut oil, whole wheat flour, and lots of dark chocolate. Wholesome AND delicious!

Yield: 12 muffins

Prep Time: 15 minutes

Cook Time: 16 minutes

Total Time: 40 minutes


  • 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 Bob’s Red Mill 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


  1. 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.
  2. 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.)
  3. 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.
  4. Divide the batter evenly between the prepared muffin cups, then sprinkle the tops with sparkling sugar. Bake the muffins for 16-18 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 in an airtight container at room temperature for up to 5 days or individually wrap and freeze for up to 3 months.

All images and text ©Erin Clarke/Well Plated.

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I am sharing this post in partnership with Bob’s Red Mill. Thanks for supporting the brands and companies that make it possible for me to continue providing quality content to you!

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About Erin Clarke

I’m fearlessly dedicated to making healthy food taste incredible. Wearer of plaid, travel enthusiast, and firmly convinced that sweets and veggies both deserve a place at the table. MORE ABOUT ERIN…


  1. The Target baking and holiday sections are very dangerous. VERY. I can’t go in there without buying everything. But that’s not a bad thing!
    These muffins look amazing. Love all that chopped chocolate!

  2. You know as a kid I thought I didn’t like gingerbread but all I had to go on were those kind of stale, crunchy gingerbread cookies for the grocery store. And of course those are terrible!! These are the opposite!! These muffins look so perfectly tender and delicious! 

  3. Gingerbread totally gets shafted this time of year compared to peppermint. I think people are afraid of it’s bold flavors. I for one love it and these muffins sound and look fantastic! Love that you used coconut sugar in them, I’ve become a huge fan of the stuff!

  4. Oh YUM! These would be so good for breakfast with a hot cup of coffee. I’m pinning this recipe immediately!

  5. Oh I with I could grab one! they look so tempting!

  6. Gingerbread can be breakfast, lunch, dinner, or dessert in my book! Pinning this. These look like they will be my favorite muffins of all time. Chocolate and gingerbread are my favs!!!!!

  7. Oh my goodness–so many of my favorite ingredients in one! I love baking with coconut oil, and I’ve recently discovered coconut sugar and am super excited about it. Plus chocolate…simply a necessity. Thanks for the recipe! 

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

  9. 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! :)

    • 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!

  10. Is there a way to may these dairy free ?

    • 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!

  11. 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!

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