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    Home » Recipes » Gluten Free Muffins & Scones

    Gluten Free Gingerbread Muffins

    Published: Dec 11, 2025 by Nicole Spiridakis

    Jump to Recipe Print Recipe

    Warmly spiced gluten-free gingerbread muffins take everything you love about classic gingerbread and turn it into a handheld snack! Yogurt, whole-grain oat flour, and a hint of molasses make these little beauties a festive and nourishing treat.

    Gluten free gingerbread muffins on plates next to a bowl of muffins.

    When December hits, I start digging into the molasses stash in my pantry, making sure I have enough of the cozy spices we all love, and whipping up pans of gluten-free gingerbread cake and gluten-free gingerbread snacking cake on the regular.

    When I want to bake something a bit more wholesome and morning-appropriate than, you know, cake, I make gingerbread muffins. Packed with whole grains, naturally gluten-free, nicely moist from plenty of yogurt, and just sweet enough, these are muffins to enjoy with a hot cuppa. Drizzle with a little lemon glaze to make them extra special.

    Jump to:
    • Why I Love These Sweet Muffins
    • Ingredients Needed
    • Step-by-Step Instructions
    • Baking Tip: Use Honey
    • Tips & Recipe Notes
    • Serving Options
    • Proper Storage
    • More Holiday Morning Recipes
    • Recipe

    Why I Love These Sweet Muffins

    These gingerbread muffins are such an easy holiday win - simple ingredients and method, a short prep time, and they are loved by both kids and adults!

    • Sturdy and packable. Oh, I do love a muffin that's great for the lunchbox! These muffins pack up so well, making them a perfect portable snack.
    • Warm and festive. There's something about classic gingerbread flavors that just sings "holiday." All the familiar flavors are here: cinnamon, ginger, cloves, brown sugar, and molasses!
    • Perfect for when you don't want to bake a whole cake. Want to nibble on gingerbread but don't feel like embarking on a cake-baking project? Gingerbread muffins hit the sweet spot between full-on cake and gingerbread goodness.
    Ingredients for gluten free gingerbread muffins are text labeled.

    Ingredients Needed

    Here's a look at what you'll need to make these muffins. Make sure to scroll down to my recipe card at the bottom of this post for the full ingredient amounts and instructions.

    • Yogurt - I like to use plain, whole milk yogurt here, but you can use low-fat or non-fat yogurt if needed.
    • Eggs - I used large eggs.
    • Butter - Unsalted butter is best, melted, then slightly cooled before adding to the batter.
    • Molasses - Either regular or blackstrap molasses works here, just note that blackstrap molasses has a slightly stronger taste.
    • Oat flour - Whole grain oat flour is my choice here for whole grain goodness and structure. Don't eat oats? Try brown rice flour or sorghum flour by weight, or substitute an oat-free 1:1 gluten-free flour blend.
    • Brown sugar - Light or dark brown sugar is fine, or try coconut sugar.
    • Baking powder
    • Spices - A mix of ground cinnamon, ginger, and cloves.
    • Salt - I always use fine sea salt, and table salt also works.
    A bowl of gluten free gingerbread muffins.

    Step-by-Step Instructions

    Here's an overview in photos of how to make gluten free gingerbread muffins:

    Flour mix and wet mix are combined in a bowl for gluten free gingerbread muffins.

    1. Mix wet ingredients: In a large bowl, whisk together the yogurt, eggs, butter, and molasses.

    The flour mix for gluten free gingerbread muffins in a bowl.

    2. Make dry mix: In another bowl, whisk together the flour, sugar, baking powder, spices, and salt. Fold this mix into the molasses mixture.

    Gluten free gingerbread muffin batter in a muffin tin.

    3. Rest: Grease a muffin tin and divide the batter equally between the muffin cups. Rest the batter for 15 minutes.

    Gluten free gingerbread muffins cool in a muffin tin.

    4. Bake: Place in a 375F oven and bake for about 20 minutes, cool in the pan, then turn out to cool completely.

    Baking Tip: Use Honey

    If you don't have molasses in the pantry, try ¼ cup of honey instead. While you won't find that deeply dark molasses-y undertone, you'll still get the general flavor of gingerbread that is very satisfying. Also, try my gluten free gingerbread loaf that's made with honey instead of molasses.

    A cup of coffee and gluten free gingerbread muffins.

    Tips & Recipe Notes

    • Adjust the amount of sugar. I admit that I do love my muffins a bit on the sweeter side, so I used ¾ cup of brown sugar here. Feel free to adjust the amount to ½ cup of sugar if you like a less-sweet muffin, or increase it to 1 cup if you like a more cupcake-like muffin.
    • Try gluten-free flour. I love swapping my homemade gluten free flour blend for the oat flour by weight, or you can use a 1:1 baking blend of your choice.
    • Top with sugar. For a little bit of crunch, sprinkle the tops of the muffins with coarse sugar before baking.
    • Dairy-free. Easily make these muffins dairy-free by substituting non-dairy yogurt for the yogurt and melted non-dairy butter or coconut oil for the butter.
    • Add chocolate. If your kids love chocolate as much as mine do, stir in ½ cup of mini chocolate chips to the batter.
    • Use pumpkin pie spice. In a pinch, swap 2 teaspoons of pumpkin pie spice for the spices.
    • Make 'em mini. Perfect for a class holiday party! Bake the batter in a 24-cup mini muffin tin. You will need to adjust the baking time since mini muffins take shorter to bake.
    A gluten free gingerbread muffin on a festive plate.

    Serving Options

    • Make them cupcakes - These can absolutely work as cupcakes, topped with cream cheese icing.
    • With butter - A little bit of softened butter on a warm muffin is so good!
    • Cream cheese - Likewise, softened cream cheese is a deliciously tangy complement to the sweet gingerbread.

    Proper Storage

    Always cool muffins thoroughly before storing them - if they are slightly warm, they will get soggy when added to a container. Here are some storage options:

    • Counter - Place the cooled muffins in an airtight container and store them on the counter for up to 3 days.
    • Fridge - Pop the container in the fridge and keep the muffins for up to 5 days.
    • Freezer - Place muffins in a freezer-safe bag and store them in the freezer for up to 2 months. Thaw in the fridge before eating.

    More Holiday Morning Recipes

    • Slices of cranberry orange bread, a cup of tea, and more slices of bread.
      Gluten Free Cranberry Orange Bread
    • Cups of tea and gluten free donut muffins.
      Gluten Free Donut Muffins
    • A gluten free orange cranberry muffin on a plate.
      Gluten Free Orange Cranberry Muffins
    • A slice of gluten free cranberry walnut bread on a plate.
      Gluten Free Cranberry Walnut Bread

    Happy baking! If you make this recipe, I'd love to know. Please leave a comment below, reach out with any questions, and tag me on Instagram @Cucina Nicolina  ❤️

    Recipe

    Gluten free gingerbread muffins on plates next to a bowl of muffins.
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    Gluten Free Gingerbread Muffins

    Nicole Spiridakis
    Warmly spiced gluten-free gingerbread muffins take everything you love about classic gingerbread and turn it into a handheld snack!
    No ratings yet
    Print Recipe Pin Recipe
    Prep Time 10 minutes mins
    Cook Time 20 minutes mins
    Total Time 30 minutes mins
    Course Breakfast
    Cuisine American
    Servings 12 servings
    Calories 191 kcal

    Ingredients
     
     

    • 1 cup plain yogurt
    • 2 eggs
    • ¼ cup unsalted butter melted and cooled slightly
    • ¼ cup molasses
    • 1 ½ cups oat flour or gluten free baking flour (180 grams)
    • ¾ cup brown sugar (light or dark brown sugar is fine)
    • 1 ½ teaspoons baking powder
    • 1 teaspoon cinnamon
    • 1 teaspoon ground ginger
    • ¼ teaspoon cloves
    • ¼ teaspoon fine sea salt

    Instructions
     

    • Grease or well-butter the cups of a standard-size muffin tin.
    • In a large bowl, whisk together the 1 cup plain yogurt, 2 eggs, ¼ cup unsalted butter, and ¼ cup molasses.
    • In a medium bowl, whisk together the 1 ½ cups oat flour , ¾ cup brown sugar, 1 ½ teaspoons baking powder, 1 teaspoon cinnamon, 1 teaspoon ground ginger, ¼ teaspoon cloves, and ¼ teaspoon fine sea salt. Gently fold the flour mixture into the yogurt mixture.
    • Divide the mixture evenly among the prepared muffin tin.
    • Preheat the oven to 375℉ and rest the batter while the oven heats. Then, bake for 15-20 minutes, or until a tester inserted into the center of a muffin comes out clean. Let cool in the pan for a few minutes, then run a knife around the edges and transfer muffins to a wire rack to cool completely.

    Nutrition

    Calories: 191kcalCarbohydrates: 30gProtein: 4gFat: 7gSaturated Fat: 3gPolyunsaturated Fat: 1gMonounsaturated Fat: 2gTrans Fat: 0.2gCholesterol: 40mgSodium: 131mgPotassium: 223mgFiber: 1gSugar: 20gVitamin A: 179IUVitamin C: 0.1mgCalcium: 95mgIron: 1mg
    Disclaimer: Nutrition information is automatically calculated and is an estimate (I'm not a nutritionist and can't guarantee accuracy!). Even when not specified, be sure to check that all the ingredients you use are gluten free if you need them to be by reading labels on all packaging and/or confirming with the manufacturer.
    Did you make this recipe?Let me know in the comments how it went!

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    Photo of Nicole Spiridakis.

    Welcome!

    Cucina Nicolina is your home for carefully tested gluten-free baking recipes made with simple, wholesome ingredients. I'm a writer, recipe developer, and cookbook author who loves to share all things yummy and gluten-free. Learn more about me.


    The cover of the cookbook Flourless: Recipes for Naturally Gluten-Free Desserts by Nicole Spiridakis shows an opera cake.

    My cookbook, Flourless, was published by Chronicle Books and is full of naturally gluten-free desserts to tempt everyone! Learn more.

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