These Healthy Gingerbread Muffins are the perfect blend of warming spices, wholesome ingredients, and nostalgic holiday flavors. Whether you’re looking for a nourishing breakfast, a cozy afternoon snack, or a festive treat that’s both delicious and satisfying, these muffins are exactly what you need.

A Gingerbread Muffin cut in half.

These Gingerbread Muffins are moist, lightly sweetened with molasses and maple syrup, and packed with the classic warming spices that make gingerbread so irresistible. Made with real eggs and Greek yogurt, these fluffy muffins have an added protein boost.

If you love the comforting aroma of ginger, cinnamon, and molasses filling your kitchen, this is the recipe for you!

I love packing these muffins in my kids’ lunchboxes! My kids also love when I make some of my other muffin recipes like my Apple Cinnamon Muffins, Banana Carrot Muffins, or Blueberry Oatmeal Muffins.

Recipe Ingredients

You’ll need the following ingredients to make these Gingerbread Muffins:

Ingredients for gingerbread muffins.

Ingredient Notes

  • Molasses: I used unsulfured blackstrap molasses, but you can use regular dark, unsulfured molasses for a bit of a sweeter taste. The molasses is packed with minerals and gives these muffins their classic dark, robust taste.
  • Eggs: These help bind the muffins and provide structure, creating a light and fluffy texture.
  • Greek Yogurt: Adds moisture and a subtle tanginess while keeping the muffins incredibly soft and delicious. Use plain Greek yogurt for the best results.
  • Spices: The combination of ginger, cinnamon, nutmeg, and cloves creates that quintessential gingerbread flavor profile. I love using Selefina Spices! Each spice plays a crucial role in developing the warm, comforting taste.

Additions & Substitutions

  • Nuts: Fold in ¼ cup of chopped walnuts or pecans for added crunch and nutty flavor.
  • Turbinado Sugar: Sprinkle the tops of the muffins with turbinado sugar before baking for some added texture and sweetness.
  • Chocolate: Fold in ¼ cup of dark chocolate chips to the muffin batter if you want to add a chocolate flavor.
  • Flour: Use a gluten-free 1:1 baking blend to make these muffins gluten-free.
  • Molasses: You can use dark, unsulphured molasses or blackstrap molasses for this recipe.
  • Milk: Any milk can be used in place of almond milk.
  • Allspice: You can replace the cinnamon, nutmeg, and ground clove for 1.5 teaspoons Allspice, if needed.

Tools For This Recipe

Gingerbread muffins on a plate.

How to Make Healthy Gingerbread Muffins: Step-by-Step

For the full recipe with the exact ingredients, scroll down to the printable recipe card below!

  • Step 1: In a large bowl, combine all-purpose and whole wheat flour, baking powder, baking soda, ginger, cinnamon, nutmeg, clove, and salt.
  • Step 2: In a medium bowl, combine yogurt, eggs, molasses, maple syrup, coconut oil, vanilla, and almond milk.
  • Step 3: Pour wet ingredients into the flour mixture and stir until just combined.
  • Step 4: Use a cookie scoop and fill each muffin liner to the brim with batter. (Optional) Top muffins with turbinado sugar or sea salt flakes.
  • Step 5: Bake in the oven at 350 degrees Fahrenheit for 17-18 minutes or until a toothpick comes out clean when inserted in the middle of the muffins.

Recipe Tips & Tricks

  • Double the Batch: These muffins freeze beautifully! Make a double batch and freeze half for quick breakfasts or snacks.
  • Make Ahead: Mix your dry ingredients and cover the night before to speed up morning preparation.

Storage & Reheating

  • Counter: Store leftovers in an airtight container on the counter for up to 2 days.
  • Fridge: Store leftovers in an airtight container in the fridge for 3-4 days. Warm slightly before serving for the best flavor.
  • Freezer: Freeze in a single layer or individually wrapped for up to 3 months. Thaw at room temperature or microwave for 20-30 seconds when ready to eat.
A stack of muffins.

Frequently Asked Questions

Can I make these muffins vegan?

To make vegan gingerbread muffins, you’ll need to replace the eggs and Greek yogurt. Try using chia eggs (2 tablespoons chia seeds + 5 tablespoons water) and a non-dairy yogurt alternative like coconut yogurt.

Can these gingerbread muffins be made gluten-free?

The recipe can be easily adapted for gluten-free diets by using a 1:1 gluten-free flour blend instead of regular flour and whole wheat flour.

What type of molasses should I use?

You can use dark, unsulphured molasses for a sweeter flavor or blackstrap molasses works as well, but won’t be as sweet (I used unsulphured blackstrap molasses in this recipe!)

More Muffin Recipes You’ll Love!

Spinach Banana Muffin cut in half with peanut butter.
Spinach Muffins for Toddlers
Banana blueberry muffins in a stack.
Blender Banana Blueberry Muffins
Pumpkin muffins on a plate.
Banana Pumpkin Muffins (GF)
Applesauce muffins on a plate.
Banana Muffins With Applesauce
Kaileigh Gaffney from Supermom Eats.

Did you try this recipe?

Let me know how you liked it by leaving a comment and rating below! Or tag me on Instagram and share what you made!

A Gingerbread Muffin cut in half.
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Healthy Gingerbread Muffins (With Greek Yogurt!)

Author: Kaileigh Gaffney
Yield: 10 muffins
These Healthy Gingerbread Muffins are perfectly spiced and naturally sweetened with molasses and maple syrup. A cozy breakfast or snack ready in under 30 minutes!
Prep Time: 5 minutes
Cook Time: 17 minutes
Total Time: 23 minutes
Print Recipe Pin Recipe Leave a Review

Ingredients
 

  • 1 cup all-purpose flour
  • ½ cup whole wheat flour
  • 1 teaspoon baking powder
  • ½ teaspoon baking soda
  • 1 teaspoon ground ginger
  • 1 teaspoon Ground Cinnamon
  • ¼ teaspoon Ground Nutmeg
  • ¼ teaspoon Ground Clove
  • ¼ teaspoon salt
  • ½ cup plain Greek yogurt
  • 2 eggs
  • ⅓ cup molasses, dark and unsulphured or blackstrap work
  • 1 tablespoon 100% pure maple syrup
  • 2 tablespoons coconut oil, melted
  • 2 teaspoons vanilla extract
  • ½ cup plain unsweetened almond milk, (or any preferred milk)
  • Optional for topping muffins Sea Salt Flakes or Turbinado sugar

Instructions
 

  • Preheat oven to 350 degrees Fahrenheit and line a muffin tray with 10 non-stick muffin liners.
  • In a large bowl, combine all-purpose flour and whole wheat flour, baking powder, baking soda, ground ginger, cinnamon, nutmeg, clove, and salt.
  • In a medium bowl, combine yogurt, eggs, molasses, maple syrup, coconut oil, vanilla, and almond milk.
  • Pour wet ingredients into the flour mixture and stir until just combined.
  • Use a cookie scoop and fill each muffin liner to the brim with batter. (Optional) Top muffins with Turbinado sugar or sea salt flakes.
  • Bake in the oven for 17-18 minutes or until a toothpick comes out clean when inserted in the middle of the muffins.
Course: Snack
Cuisine: American
Diet: Vegetarian
Calories: 152kcal, Carbohydrates: 25g, Protein: 4g, Fat: 4g, Saturated Fat: 3g, Polyunsaturated Fat: 0.4g, Monounsaturated Fat: 1g, Trans Fat: 0.004g, Cholesterol: 33mg, Sodium: 193mg, Potassium: 235mg, Fiber: 1g, Sugar: 10g, Vitamin A: 49IU, Vitamin C: 0.01mg, Calcium: 86mg, Iron: 2mg
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