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.

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.
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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 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.

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

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

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

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

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.

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.

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
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
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.









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