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In the rush between pumpkin-spiced October and cookie-studded December, November can be easy to miss. Before the month passes me the way that most have lately—in a total blur—I’d like a take a moment to celebrate November with Gingerbread Apple Muffins.

Healthy, moist Gingerbread Apple Muffins. Easy, delicious recipe made with whole wheat flour, coconut sugar, and warm holiday spices. Perfect breakfast recipe for Christmas morning, Thanksgiving, and last-minute holidays guests!

These sky-high muffins are moist, healthy, and an ideal bridge between the fall that is still here and the holidays that are to come. Made with molasses, whole wheat flour, and a heap of holiday spices, their flavor is rich, warm, and even tempted me to turn on the Christmas music (too soon?).

At the same time that these muffins ring a holiday bell, however, they also honor fall. I squeezed every bit of sweet, crisp apple into the batter that it could possibly hold. The result is a fruit-studded, cinnamon-spiced muffin that’s part harvest, part holiday, and wholly November.

Moist Gingerbread Muffins made with molasses, whole wheat flour, and warm holiday spices. Easy, healthy recipe that’s perfect for Christmas morning or Thanksgiving!

Making Gingerbread Apple Muffins

The recipe for these Gingerbread Apple Muffins are based off of my favorite Dark Chocolate Gingerbread Muffins. Although I fully support muffins studded with melting puddles of dark chocolate at breakfast, that extra indulgence feels a little more December to me. It’s still November, so for now, I’m still all about the apples.

I *did*, however, keep the sparkly sugar muffin topping.

Although it is optional, the muffins themselves are not very sweet, so I find it provides the right balance. I’m also completely smitten with the way the sugar turns into a yummy, lightly crunchy “lid” that I can pull apart with my fingers.

Also, the sparkle. ? The holidays are coming, after all.

These Coffee Cake Muffins are another delicious, festive muffin recipe for cinnamon spice lovers.

Moist Gingerbread Muffins. Easy, healthy recipe that's perfect for a holiday morning!

These Gingerbread Apple Muffins are freezer friendly, so if you are baking a batch (or a double batch), you can easily stow some away for quick, healthy breakfasts later on and for holiday guests too.

I have everything you need to know about storing and freezing muffins in my guide How to Store Muffins, so be sure to check it out as well.

More Delicious Muffin Recipes

Cinnamon and Ginger Muffins recipe – Healthy, moist, and so easy to make! Made with whole wheat flour, molasses, Greek yogurt, and warm holiday spices.

Recommended Tools to Make This Recipe

  • Muffin tins: I love these for their handy lid and these for their even baking.
  • Large scoop: My secret to tall, extra-fluffy muffins.

Gingerbread Apple Muffins

4.72 from 7 votes
Healthy, moist Gingerbread Apple Muffins. Easy, delicious recipe made with whole wheat flour, molasses, and lots of warm holiday spices.

Prep: 15 minutes
Cook: 17 minutes
Total: 40 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 1/2 cups  white whole wheat flour
  • 1 cup all-purpose flour
  • 1 1/2 teaspoons baking soda
  • 1 1/2 teaspoons ground ginger
  • 1 1/2 teaspoons ground cinnamon
  • 1/2 teaspoon kosher salt
  • 1/4 teaspoon ground cloves
  • 1 1/2 cups finely diced sweet-crisp apples such as Pink Lady or Honeycrisp, peels on (about 1 medium)
  • Optional: Sparkling or turbinado raw 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 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 medium 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. If this happens, gently warm the bowl in the microwave in 30-second bursts, just until it melts.)
  • In a separate, large bowl, whisk together the white whole wheat flour, all-purpose flour, baking soda, ginger, cinnamon, salt, and cloves. Fold in the diced apples, stirring gently to coat.
  • Pour the wet ingredients into the dry and stir gently by hand, just until the flour disappears. The mixture will be lumpy and thick, but do not overmix.
  • Divide the batter evenly between the prepared muffin cups (I like to use a large scoop like this, as it helps the muffins rise the best), then sprinkle the tops with sparkling sugar, if desired. 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.




Serving: 1muffinCalories: 223kcalCarbohydrates: 38gProtein: 5gFat: 6gSaturated Fat: 4gCholesterol: 16mgSodium: 223mgFiber: 3gSugar: 19g

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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

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  1. These muffins look amazing….I want to try them but wondering if there is a substitute for the greek yogurt. I was thinking maybe applesauce?

    1. Hi Laura, I think sticking to Greek yogurt is the safest bet, because it’s much thicker than applesauce and gives the muffins more structure and moisture than applesauce would. You could try playing around with half applesauce half yogurt to start, but the only way I can recommend is with yogurt, since that is what I tested. I hope you enjoy!

  2. I’m so excited by this recipe that I’m going to buy some sparkling sugar (why not?) this weekend to make them! I have everything else. yum!!!

      1. They were fantastic, by the way! It might be my favorite recipe yet. And that’s saying A LOT as I’m a pumpkin fanatic so usually those are my favorite recipes!

  3. I just made these and they are deeeeelicious! They definitely taste better when they are totally cooled down. (I couldn’t help but try them fresh out of the oven bc they smelled so good but it’s worth the wait). I ran out of eggs so made a chia egg and that worked just fine (mixed 1tb chia with 2.5 tb water and let sit for 5 min). Cut the sugar in half and used honey instead of molasses bc didn’t have any and it also worked. Maybe not the most potent/authentic taste as if I had molasses but they still came out great. The texture is chewy just like you’d want a gingerbread to be. The apples are divine in this. There was lots more batter than my usual muffin batter but I just piled them high bc it’s so thick it doesn’t run over and am glad I did rather than filling a second pan. Makes huge delicious muffins. Definitely a repeater! 5 stars

  4. As in the above comment, I thought I’d measured something incorrectly when I had so much batter – but just kept piling it in with hopes of them not spreading all over my nice clean oven. They turned out looking just like the huge ones you can get at the bakery and the taste was wonderful. I love gingerbread but these were much more “gourmet” than a plain pan of gingerbread.4 stars

    1. Chris, I’m happy to hear the recipe was a success and that you enjoyed the muffins! Thanks so much for chiming in with your review!

  5. I just made these and they were absolutely fantastic! My co-interns and I have been having a rough week, and I decided we needed some comfort food to round out the week. These had the all comfort of a winter treat with the sweetness and “health” of the apple so I don’t feel terrible eating them. I will definitely be making these again!5 stars

    1. Melanie, I’m so happy to hear these muffins could be a bright spot in your week! Thanks so much for giving the recipe a try!

  6. I just made these for a pre-holiday treat with the last of my orchard apples. SO. GOOD. Moist and delicious!! I subbed EVOO because i had it and turned out great.  Thanks for another FABULOUS muffin recipe! If I could gibe it more than 5 stars, I would. (P.S. I just ate one, could not help myself!)5 stars

  7. These muffins are delicious! I didn’t have white whole wheat flour, so I used regular whole wheat instead. And it definitely helped to let the cold ingredients come to room temp first. They turned out great!5 stars

    1. Hi! Blackstrap molasses behaves quite differently in baking and tastes a lot different than regular molasses (it’s bitter and salty by comparison), so regular molasses is what you’ll want to use here. Enjoy!

  8. These are the most flavorful muffin! I couldn’t remember if I had already left a review as this is my second time to make them. This is now my 13yr old daughters favorite muffin! I used a brown sugar substitute and loved it! Love the extra protein from the Greek yogurt !!5 stars

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