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Overhead view of sourdough gingerbread muffins on parchment paper, some drizzled with creamy eggnog icing, others dusted with powdered sugar, and one muffin cut in half to show its moist interior.
Sourdough Discard Muffins

My Sourdough Gingerbread Muffin Recipe with Eggnog Icing

This sourdough gingerbread muffin recipe blends organic ingredients and warm spices for a wholesome, cozy and festive treat.

Prep: 10 minutes
Cook: 30 minutes
Total: 40 minutes
Jump to Recipe Rate Recipe
Recipe Index | Ferment | Sourdough Discard | Sourdough Discard Muffins

My Sourdough Gingerbread Muffin Recipe with Eggnog Icing

This sourdough gingerbread muffin recipe blends organic ingredients and warm spices for a wholesome, cozy and festive treat.

Overhead view of sourdough gingerbread muffins on parchment paper, some drizzled with creamy eggnog icing, others dusted with powdered sugar, and one muffin cut in half to show its moist interior.

Healthy Gingerbread Muffins

There’s something truly special about homemade treats during the holiday season, and you’re going to love this sourdough gingerbread muffin recipe. The gingerbread muffins are the perfect way to bring warmth and comfort to your kitchen this holiday season.

These muffins are made with wholesome, organic ingredients and feature a hint of tang from sourdough. They combine the rich spices of ginger, nutmeg, and allspice with the natural depth of sourdough starter. Whether you’re baking for a cozy breakfast, a holiday gathering, or to fill your home with festive flavors, these muffins provide a nourishing twist on a classic favorite.

Close-up of sourdough gingerbread muffins on crinkled parchment paper, featuring muffins drizzled with eggnog icing, dusted with powdered sugar, and one muffin cut in half to reveal its spiced, moist texture.

Sourdough Gingerbread Muffin Recipe Ingredients

Here is a list of all the ingredients you need to bake these delicious sourdough gingerbread muffins! Note that I use a mix of whole wheat and all-purpose flour in this recipe, but you can use just all-purpose with great results.

  • all-purpose flour
  • whole wheat flour
  • brown sugar
  • powdered sugar
  • baking soda & baking powder
  • ground Ginger
  • allspice
  • nutmeg
  • cinnamon
  • salt
  • organic molasses
  • grass-fed butter
  • sourdough starter
  • vanilla extract
  • whole milk
  • 2 eggs
  • eggnog
Overhead view of a mixing bowl with dry ingredients for sourdough gingerbread muffins, including whole wheat flour, all-purpose flour, brown sugar, baking soda, and spices like ginger and cinnamon.
Mixing bowl with wet ingredients, including molasses, sourdough starter, and melted butter, being combined with the dry ingredients.
Thick and spiced sourdough gingerbread muffin batter being mixed with a wooden spoon in a white mixing bowl on a marble countertop.

Using Sourdough Discard in Muffins

The fermentation process used to create sourdough bread enhances its nutritional profile. Sourdough is easier to digest than traditional yeast bread. In sourdough, lactic acid bacteria break down gluten, fructans, and phytic acid. This can be particularly beneficial for individuals with gluten or FODMAP sensitivities.

Muffins are not usually long-fermented, but they can be! I don’t long ferment these gingerbread muffins, but many readers have told me they have successfully fermented the batter overnight in the fridge for easier digestion. You can try fermenting the muffin batter overnight in the refrigerator before preheating your oven and filling your muffin tin with batter.

Gingerbread Muffin Recipe with Eggnog Icing

Eggnog mixed with powdered sugar makes a fantastic icing for gingerbread muffins. It enhances the flavor and creates a beautifully smooth and sturdy finish. Unlike traditional milk-based icings, eggnog creates an icing that dries more effectively. The rich, spiced flavor of eggnog complements the warm spices in the gingerbread, adding a festive depth to each bite. This icing offers a subtle sweetness and creaminess that pairs perfectly with the muffins’ bold flavors of ginger, cinnamon, and cloves.

Gingerbread Muffin Recipe Tips

One crucial tip when making these sourdough gingerbread muffins is to avoid overmixing the batter. Overmixing can result in dense muffins rather than light and fluffy protein muffins, and the reason behind this is the formation of gluten.

Gluten, a protein present in flour, gives structure to baked goods. However, excessive mixing develops gluten strands, leading to a denser texture. To prevent this, gently mix the dry and wet ingredients until they are just combined, ensuring there are still some lumps and streaks of flour in the batter.

This technique allows the muffins to rise correctly, resulting in a tender crumb.

My other muffin baking tip is always to use a thin metal aluminum muffin tin with paper liners. A metal muffin tin works way better than a silicone muffin pan.

Storing Gingerbread Muffins

Storing baked sourdough gingerbread muffins properly ensures they remain fresh and delicious. Here are some tips on how to store them effectively:

  • Room Temperature Storage:
    • Allow muffins to cool completely.
    • Place them in an airtight container lined with paper towels to absorb excess moisture.
    • Store at room temperature for up to 3-4 days.
  • Refrigeration:
    • If the weather is hot or humid, consider refrigerating the muffins.
    • Store in an airtight container in the fridge for up to one week.
  • Freezing Muffins:
    • Cool muffins completely before freezing.
    • Place muffins in a freezer-safe bag or container.
    • Label it with the date and freeze it for up to 3 months.
  • Reheating Frozen Muffins:
    • Remove the desired number of muffins from the freezer.
    • Microwave on high for 20-30 seconds or until warm.
    • Alternatively, preheat the oven to 350°F (175°C) and heat muffins for 10-15 minutes until warmed.

Gingerbread Muffin Recipe FAQ

What’s the secret to moist muffins?

The key to moist muffins is preventing them from frying out. Here are some common issues and solutions:

  • Low-Fat Ingredients: Low-fat substitutes can reduce moisture. This recipe uses grass-fed butter to keep muffins moist.
  • Too Much Flour: Over-measuring flour can make muffins dry. Use the spoon-and-level method for accuracy.
  • Overmixing: Mixing the batter too much can develop excessive gluten, resulting in dense muffins. Mix until just combined.
  • Baking Time: Baking for too long can dry out muffins, and every oven runs at a slightly different temperature. Check them a few minutes early with a toothpick; it should come out clean but not dry.

What temperature do you bake muffins at?

For best results, I bake muffins at 350° F. I always use my Breville smart oven to bake smaller items like muffins, and it works perfectly every time.

More Sourdough Muffin Recipes

  • Cottage Cheese Pumpkin Protein Muffins with Sourdough Discard
  • Double Chocolate Cherry Muffins with Sourdough Discard
  • Oatmeal Chocolate Chip Muffins with Sourdough Discard
Overhead view of sourdough gingerbread muffins on parchment paper, some drizzled with creamy eggnog icing, others dusted with powdered sugar, and one muffin cut in half to show its moist interior.
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Overhead view of sourdough gingerbread muffins on parchment paper, some drizzled with creamy eggnog icing, others dusted with powdered sugar, and one muffin cut in half to show its moist interior.
Sourdough Discard Muffins

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5 from 1 review

My Sourdough Gingerbread Muffin Recipe with Eggnog Icing

This sourdough gingerbread muffin recipe blends organic ingredients and warm spices for a wholesome, festive treat that’s perfect for a cozy holiday gathering, a warm snack, or a Christmas breakfast!

  • Prep: 10 minutes
  • Cook: 30 minutes
  • Total Time: 40 minutes

Ingredients

Gingerbread Muffins

  • 1 1/4 cup all-purpose flour
  • 1 cup whole wheat flour
  • 1/4 cup brown sugar, packed
  • 1/2 teaspoon baking soda
  • 1 teaspoon baking powder
  • 1 tsp ground ginger
  • 1/2 tsp cinnamon
  • 1/4 tsp allspice
  • 1/4 tsp nutmeg
  • 1 teaspoon salt
  • 3/4 cup molasses
  • 1/2 cup grass-fed butter, melted, room temperature
  • 1/2 cup sourdough starter, room temperature
  • 2 teaspoons vanilla extract
  • 1/3 cup whole milk, room temperature
  • 2 eggs, room temperature

Eggnog icing

  • 1/2 cup powdered sugar
  • 2 tablespoons eggnog

Instructions

  1. Preheat your oven to 350° F.
  2. Line a muffin tin with paper liners.
  3. In a medium-large mixing bowl, combine the flour, sugar, baking soda, baking powder, ginger, cinnamon, allspice, nutmeg, and salt.
  4. In a separate bowl, combine the molasses, butter, sourdough starter, vanilla, milk, and two eggs. Whisk until combined. The butter may be clumpy, this is fine and helps keep the muffins moist.
  5. Gently fold the wet ingredients into the dry ingredients until everything is just combined. Do not over-mix. The batter should be thick, and it’s okay if there are clumps.
  6. Spoon the batter into the lined muffin tins.
  7. Bake for about 30 minutes total. Rotate the pan halfway through.
  8. Allow to cool completely before topping with icing.
  9. To make the icing, combine the eggnog and powdered sugar in a small bowl.

Did you make this recipe?

Please leave a 5-star review below if you loved it! Tag @cultured.guru on Instagram

 

Nutrition information is auto-calculated and estimated as close as possible. We are not responsible for any errors. We have tested the recipe for accuracy, but your results may vary.

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Kaitlynn Fenley Author, Educator, Food Microbiologist
Kaitlynn is a food microbiologist and fermentation expert teaching people how to ferment foods and drinks at home.
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  1. Courtney
    09|29|2025

    These are so yummy! Ended up pulling mine at 25 minutes and they are so perfect and moist inside. Not too sweet at all. I ended up making my icing with maple syrup since eggnog isn’t quite in season yet!

    Reply

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A lot of people think vinegar kills all microbes b A lot of people think vinegar kills all microbes because shelf stable pickles do not contain microbes. But with shelf stable pickles, it’s the pasteurization/sterilization via hot water bath or pressure canning that makes shelf stable pickles free of microbes.

Hot hot hot acid in a pressurized environment does kill, well…most microbes. 

Think about “refrigerator pickle” recipes, though. They need to be stored in the refrigerator because vinegar alone doesn’t stop fermentation.

Fridge pickles are made without pasteurization/sterilization (canning) so they will wild ferment without refrigeration, and not necessarily in a good way because there’s not enough salt. 

All vinegar is made via fermentation too, and vinegar fermentation involves acetic acid bacteria, but also a ton of LAB, mainly Lactobacillus, Pediococcus, and Leuconostoc (the same genera you’d find in fermented veg.)  I linked a reference paper in my fermented mushroom recipe blog, so you all can read about the LAB involved in vinegar fermentation. 

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#mushrooms #fermentation
I will not ever wild lacto ferment just beets agai I will not ever wild lacto ferment just beets again lol. Mixing with cabbage for beet sauerkraut is the best though! 

“Lacto fermented beets” was the first ferment I tried to make after learning sauerkraut in college. My best friend Sidney came over and we used these gorgeous beets from the farmers market, with 2.5% salt, and some spices. Well, it ended up tasting like beet moonshine and it was just… not good.

But it was a conduit for learning. Those beets were my first lesson in how different sugars and growth in the rhizosphere vs the phyllosphere influences fermentation. 

Cabbage and the cabbage microbiome offer a lot to balance out beets in fermentation, and I think mixing into a sauerkraut is the only way to go for lacto fermenting beets! 

Try googlin’ “beet and red cabbage sauerkraut” and you’ll see my recipe, I’m Cultured Guru.
Squash is the secret ingredient! My Roasted Butte Squash is the secret ingredient!

My Roasted Butternut Squash Hot Sauce recipe is free on my website! I didn’t cook this one, so yes it’s still probiotic.

When lactic acid bacteria ferment the starches in winter squash, they naturally convert them into emulsifying compounds called exopolysaccharides. So when we blend our hot sauce after fermentation, there’s no watery separation in the bottle. Roasting the squash with the garlic for the recipes also adds such good flavor! 

Definitely make sure it’s fully fermented and not bubbling anymore before you blend and bottle. Otherwise, it’ll carbonate in the cute little hot sauce bottles.

#hotsauce
Myth Busting: Yes, the SCOBY IS the pellicle! Plee Myth Busting: Yes, the SCOBY IS the pellicle! Pleeeease stop saying it’s not. 😌



Watch till the end, I show you how to grow one!



This is a little tidbit from what I teach in the Kombucha lesson in our Fermented Drinks Semester online course!

I also share this recipe FOR FREE just ✨GOOGLE✨ “cultured guru SCOBY” and you’ll see my full recipe with the perfect sugar to tea ratios for growing, feeding and maintaining a kombucha SCOBY.

#kombucha
And the knife stays in the box. GOOGLE “sourdoug And the knife stays in the box. 

GOOGLE “sourdough king cake” my recipe is the first one! 👑☂️💚✨

If you’re like me and prefer from scratch, homemade everything, you’ll definitely want to try this king cake for Mardi Gras! I used organic naturally dyed sprinkles and all that jazz too. 

If you just search “sourdough king cake” on google you’ll see my recipe, it’s usually the first one. 

My main tips for making this:
✨use a very active starter or throw in some instant yeast with your starter
✨make sure the dough is actually proofed before shaping it. If it’s cold in your house it will take longer. 
✨please follow directions! You can cold ferment the dough in the fridge after it doubles in size and BEFORE filling and shaping.

🎵Song is Casanova by Rebirth Brass Band
Fermentation is a gift from the microbes of this e Fermentation is a gift from the microbes of this earth.

When we had a food business, I could never shake the feeling that fermentation is not meant to be sold to you from a fluorescently lit grocery shelf in an endless cycle of waste. Fermentation is meant to be cultivated in your home, with your hands, with intention and love in a sustainable, grateful practice of reciprocity and nourishment. 

This is the story of how we got here. 

After so many lessons learned, our small fermentation business is now value aligned, peaceful, fulfilling, and happy.  It often seems like the gut feelings (the microbes within us) guided us in the right direction. To teach. 

You can learn for free on our blog, or you can enroll in our online courses (we extended our new year sale!) Either way, with me as your teacher, you’ll learn to adopt a holistic perspective on the microbial ecosystems that influence our food, lives, and the planet.
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