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Warm gingerbread is a classic flavor and smell for the holiday season. Capture all of the flavor, but add protein and lose some of the calories with these Healthy Gingerbread Muffins.

You don’t have to sacrifice your favorite flavors during the holidays. Just give them a little reworking to make them more nutritious. These gluten-free gingerbread muffins use almond flour, eggs, and a dairy-free collagen glaze to increase the protein and fiber content while decreasing the sugar and calories. The result is rich, flavorful muffins that taste like the holidays, but will leave you feeling satisfied without a sugar crash.
If you like healthy gingerbread recipes, you will love my salted gingerbread cookies and gingerbread protein brownies!
Why You’ll Love This Recipe
- Classic Flavor: These delicious muffins are packed with the classic gingerbread flavor we all love from the molasses, ginger, and other warm winter spices.
- Full of Fiber and Protein: Not only are these healthy muffins totally gluten-free, but they have plenty of fiber and over 5 grams of protein.
- Bake In Less Than 15 Minutes: These delicious winter muffins are ready in less than 15 minutes! They are perfect for when you’re meal prepping or making a snack in a hurry.
Table of Contents
Ingredients

- Almond Flour: This gluten-free flour has both fiber and protein, which makes it a healthier and more satisfying choice to help fuel your day.
- Coconut Flour: This flour is also high in fiber, and it’s low-carb, so it’s great for Paleo diets. It absorbs a lot of moisture, so it’s best to blend it with another flour for baking.
- Olive Oil: Moisten the batter for your gingerbread muffins with olive oil. You could also use avocado oil or coconut oil, though the coconut oil may add too much coconut flavor.
- Molasses: This thick, dark syrup is made from boiling sugarcane but this concentrated form is actually rich with iron, calcium, and potassium. It gives gingerbread its signature flavor.
- Eggs: Not only do eggs act as a binder in baking, but they also add protein to your batter.
- Spices: Since gingerbread is known for being spicy and flavorful, you’ll need vanilla extract, ginger, cinnamon, nutmeg, and cloves to make this recipe.
- Collagen Glaze: Collagen helps support your bone density, skin firmness, and hair and nail health, especially as you age. This glaze is a simple mixture of collagen powder and unsweetened almond milk that you drizzle over your muffins.
See the recipe card below for exact ingredient amounts, nutritional information, and detailed instructions.
Variations & Dietary Modifications
- Add Chocolate: Everything tastes better with chocolate! Try these muffins with chocolate chips mixed into the batter. They will turn out similarly to my chocolate gingerbread loaf.
- Mix In Nutes: Give your muffins a little crunch by mixing walnuts or pecans into the batter.
- Try a Zero Calorie Sweetener: While I don’t recommend skipping the molasses, you can replace the honey with stevia or a different zero-calorie sweetener.
How to Make Healthy Gingerbread Muffins
If you love baking around the holidays, these healthy muffins are the perfect snack to make! You can enjoy them with breakfast, as a snack, or as a sweet treat after dinner. You just need a muffin tin sprayed with nonstick cooking spray and an oven preheated to 350°F.

Step 1: Combine the Wet Ingredients. Combine the eggs, honey, molasses, and vanilla in a large bowl. Mix them using a hand mixer or a stand mixer.

Step 2: Mix the Dry Ingredients. Whisk together the spices, flours, and baking soda in a separate bowl.

Step 3: Combine All of the Ingredients. Add half of the mixed dry ingredients to the wet mixture and stir to combine. Then add the oil and the remaining flour mixture and stir until combined. The muffin batter will be thick.

Step 4: Fill the Muffin Tin and Bake. Pour the mixture evenly into each muffin cavity and bake the muffins for 15 minutes at 350°F or until a toothpick can be inserted and removed clean.

Step 5: Drizzle with Glaze. Allow the muffins to cool, then prepare the collagen glaze by stirring the collagen powder into the almond milk. Drizzle the glaze over the top of each muffin.
Recipe Tips
- Use Room Temperature Eggs: It’s best to bake with room temperature eggs to ensure they mix evenly into the batter and don’t clump.
- Measure Properly: When measuring out gluten-free flours, it’s important to measure them properly. I recommend using a spoon to fill your measuring cup with flour and then leveling it off, versus scooping flour straight from the bag and packing it in. See my tutorial for measuring flours properly for baking for more tips for gluten-free baking!
- Whisk the Dry Ingredients: Use a whisk to mix the dry ingredients and ensure the spices are well incorporated into the flour. This helps you avoid pockets of spices in your muffins.
- Storing: Keep the gingerbread muffins in an airtight container in the refrigerator for up to 5 days. You can also wrap each muffin in plastic cling wrap and store them in a freezer-safe container for a month.

Serving Suggestions
Fluffy gluten-free gingerbread muffins are one of my favorite holiday breakfasts. They taste amazing with a cup of coffee for breakfast or with some hot cocoa in the afternoon. Everyone will love having these muffins as part of their holiday celebrations!
- Make the perfect holiday breakfast and pair your gingerbread muffins with a latte with low calorie gingerbread coffee creamer or a skinny peppermint mocha.
- Muffins may not be enough breakfast to fuel your day, but you can pair them with my sausage hash brown casserole for a fulfilling and protein-packed meal!
- If you’re meal prepping your muffins for breakfast or snacks to carry on the go, try making my protein breakfast sandwiches to go with them!
Healthy Gingerbread Muffins Recipe FAQs
If you can’t eat coconut, you could try substituting arrowroot powder, tapioca flour, or ground flax instead to create a similar texture.
I haven’t tested this recipe using flax eggs, but I think the muffins would turn out gummy from 3 flax eggs. If you try an egg substitute, let me know how it turns out!
You could use a 1:1 gluten-free flour in place of the almond flour. You’ll still need the coconut flour to achieve the correct texture in the muffins.

More Delicious Healthy Muffin Recipes
If you tried this Healthy Gingerbread Muffins recipe or any other recipe on my website, please leave a 🌟 star rating and let me know how you go in the 📝 comments below.

Healthy Gingerbread Muffins
Ingredients
- 2 cups Almond Flour
- 2 tablespoons Coconut Flour
- ⅓ cup Extra Virgin Olive Oil, or oil of choice
- 2 tablespoons Honey
- 2 tablespoons Blackstrap Molasses
- 1 teaspoon Vanilla Extract
- 3 Eggs
- 1 tablespoon Ground Ginger
- 1 teaspoon Cinnamon
- ¼ teaspoon Nutmeg
- ¼ teaspoon Cloves
- 1 teaspoon Baking Soda
For the Glaze
- 1 tablespoon Collagen
- ⅛ cup Unsweetened Almond Milk, or milk of choice
Instructions
- Preheat oven to 350 and lightly spray a muffin tin with nonstick cooking spray.
- Using a standing mixer or hand mixer, blend together the eggs, oil, honey, molasses, and vanilla until smooth.
- In a separate bowl, stir together the spices, flours, and baking soda.
- Add half the flour mixture to the liquid mixture and stir to combine. Then stir in the oil and remaining flour.
- Divide the mixture evenly among 12 muffin cavities. Bake 15 minutes at 350 F or until a toothpick can be inserted in the center clean.
- Cool the muffins on a wire baking rack. While the muffins cool, prepare the optional frosting by stirring the ingredients together. Drizzle the muffins with the frosting.
Notes
- Be sure to use room temperature eggs to avoid any clumps and ensure a smooth batter and fluffy muffins.
- Use a spoon to scoop out the flour and level it off instead of scooping it from the bag to ensure proper measurements. See my tutorial for measuring flours properly for baking for more tips for gluten-free baking!
- Whisk the dry ingredients together to avoid clumps of spices in your batter and muffins.
- Store in the refrigerator in an airtight container up to 7 days or in the freezer 30 days.
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.















Where does the extra virgin olive oil go?
It should be in step 2 with the other wet ingredients. Hope that helps!
Hi Megan….when making these muffins, I made a few changes to serve my needs better….I decreased the amount of ginger to 2 teaspoons and use 4 tablespoons of honey instead of the blackstrap molasses. Molasses has high fructose corn sugar in it, I prefer more organic ingredients and I add about 1/4 cup raisins and a 1/4 cup of chopped walnuts. Makes a very yummy muffin. I cut one in 1/2 and use about a 1/2 teaspoon of peanut butter on each half. Oh my goodness, is that delicious or what. All my favorite things rolled up in one very tasty muffin. Thank you for a great recipe. I make them all the time.
Hi Megan
Could I use anything in place of coconut flour? My son can’t eat anything coconut.
I would try to replace it with arrowroot powder, tapioca flour or ground flax.
Awesome recipe! Delicious. Thank you.
Delicious. Fast. GF/LOW CARB! WIN*WIN*WIN
These were wonderful! Would definitely make again. I thought they had the right amount of ginger flavor & they were not too sweet.
Hi I was wondering how can I properly store these in the freezer ?
You can store them in a plastic bag in the freezer.
I’m sitting here so hungry and I wish one of these was in front of me right now!! So scrumptious!
Hehe I know what you mean!
I can’t wait for you to share the meal plans. That’s so exciting!!
I am too!!! Thanks friend!
What a great idea to use collagen to make your frosting. Thanks for sharing. Sounds like you guys had a lovely weekend!
Yes! Sounds like you did too!!!