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These Healthy Gingerbread Muffins are made with molasses, coconut sugar and warm spices like ginger, cinnamon, nutmeg and cloves. They’re soft and moist inside, lower in sugar than a lot of muffin recipes and take about 30 minutes to make.

Notes From My Kitchen
I make these healthy gingerbread muffins every year around the holidays. They’re simple to make, they’re lower in sugar than a lot of other muffin recipes, and they have a really soft, moist texture inside.
I tested them with both coconut sugar and brown sugar, and both work well, so use whichever you have on hand.
They’re perfect with a mug of my Homemade Chai Tea Latte, and if you’re in a gingerbread mood, bake a batch of my Healthy Gingerbread Cookies too.
Recipe Highlights
- Cozy gingerbread flavour: four warm spices plus molasses in every bite.
- Dairy-free as written: made with coconut oil and almond milk.
- No mixer needed: just two bowls and a whisk.
- A holiday breakfast favourite: serve them with my Gingerbread Latte for the full gingerbread experience.
Key Ingredients And Substitutions
- Flour: all-purpose flour gives you the softest muffins. For more whole grains, use half all-purpose and half whole wheat flour, or half all-purpose and half oat flour like in my Oat Flour Banana Muffins.
- Molasses: I like blackstrap molasses for a bolder flavour and a darker, richer colour, but regular molasses works too. It’s the same molasses I use in my Chewy Ginger Molasses Cookies.
- Coconut oil: melt it and let it cool slightly before mixing it with the eggs so they don’t start to cook.
How To Make Healthy Gingerbread Muffins
*This is a recipe overview. The full recipe with measurements and instructions can be found below in the recipe card.
Step 1
Stir the flour, coconut sugar, spices, baking soda and salt together in a bowl.


Step 2
In a separate bowl, whisk together the coconut oil, eggs, molasses and almond milk.


Step 3
Combine the wet and dry ingredients and gently fold them together until just combined.


Step 4
Fill lined muffin cups two-thirds of the way full and bake at 350°F for 15 to 20 minutes, until a toothpick comes out clean.


How To Store
Store the muffins in a sealed container on the counter for up to 5 days, or freeze them for up to 2 months. Let frozen muffins thaw on the counter, or warm them in the oven for a few minutes before serving.
Jess’s Tips
- Don’t overmix: fold the batter just until combined. Overmixing makes the muffins dense.
- Don’t overfill the cups: fill them two-thirds to three-quarters of the way full so the muffins don’t overflow.
- Add a crunchy top: sprinkle the muffins with a little raw cane sugar before baking for an extra hint of sweetness.
- No muffin liners? Grease the pan with cooking spray and add the batter right to the pan.
- Want more muffins for the freezer? My Healthy Pumpkin Banana Muffins With Streusel freeze just as well.
Frequently Asked Questions
Yes! Swap the eggs for 2 flax eggs (2 tbsp ground flaxseed mixed with 6 tbsp water and left to gel for 5 minutes). They’re already dairy-free.
Yes, use a 1-1 gluten-free flour blend in place of the all-purpose flour.

Try These Gingerbread Recipes Next!
If you tried these Healthy Gingerbread Muffins leave a review below and tag me @choosingchia on Instagram, TikTok, or Facebook I love seeing your recreations!
Healthy Gingerbread Muffins
- Prep Time: 15 minutes
- Cook Time: 15 minutes
- Total Time: 30 minutes
- Yield: 12 muffins
- Category: Dessert
- Method: Bake
- Cuisine: American
- Diet: Vegetarian
Description
These Healthy Gingerbread Muffins are soft, moist and lower in sugar, made with molasses, coconut sugar and warm spices. They’re perfect for a cozy holiday breakfast or snack!
Ingredients
- 2 cups all-purpose flour (Can sub 1-1 gluten free flour)
- 1 tsp baking soda
- 1 tsp cinnamon
- 3 tsp ground ginger
- 1/2 tsp ground nutmeg
- 1/4 tsp ground cloves
- 1/4 tsp salt
- 1/2 cup coconut sugar
- 2 eggs
- 1 cup almond milk
- 1/2 cup coconut oil, melted and cooled.
- 1/3 cup molasses
Instructions
- Preheat the oven to 350 degrees F and line a muffin pan with paper liners.
- Mix the dry ingredients together in a bowl and the wet ingredients together in a separate bowl.
- Pour the dry ingredients into the wet, adding one third of the flour mixture at a time, and mix until just combined.
- Fill each muffin cup two-thirds to three-quarters of the way full with batter (don’t fill them more, or the muffins will overflow).
- Bake for 15 to 20 minutes, or until a toothpick comes out clean.
Notes
- Coconut sugar and brown sugar both work well in this recipe.
- For more whole grains, use half all-purpose flour and half whole wheat or oat flour.
- Use blackstrap molasses for the best flavour and a darker colour.
- To make it vegan, use 2 flax eggs (2 tbsp ground flaxseed mixed with 6 tbsp water, left to gel for 5 minutes).
- Don’t overmix the batter, or the muffins will be dense.
Storage
Store in a sealed container on the counter for up to 5 days, or freeze for up to 2 months.
Nutrition
- Serving Size: 1 muffin
- Calories: 240
- Sugar: 12g
- Fat: 12g
- Saturated Fat: 10g
- Carbohydrates: 30g
- Fiber: 4g
- Protein: 4g






















These are amazing! Perfect texture and just the right amount of sugar. So good!!
Happy you enjoyed Jana!
Hi tried this today. Quite a healthy muffin not very sweet and subtly spicy – will give these to my toddler and child for brekkie with some banana and cream cheese.
Hi Nicola, thank you for the feedback! Happy to hear you and your toddler enjoy the recipe!
Hi, I made these muffins today, they are delicious, fluffy and light. Not too sweet and the flavors are subtle enough to enjoy a few of them in one sitting, haha!
Hi Christiane! I’m so happy you enjoyed them! They’re one of my favourites to make in the winter..so warming!
Hi, I loved the recipe but a question… is the ginger fresh ginger or ginger powder?
Thank you
Hi Nadi,
I use ginger powder, but these would be delicious with fresh ginger as well!
These look delicious. Can I use oat flour instead of the spelt? Thanks.
Hi Mari! I haven’t tried using oat flour instead but if you do the consistency would probably be a bit more “gummy” or gooey texture!
Omg I made these just before and they’re so delicious and the right amount of spice and sweetness, very moist! Would be yum to have as a warm dessert with some sort of healthyish Icecream. Love these
Thanks so much Emma! Really glad you enjoy them. And that sounds delicious to have them with ice cream, a little treat! 😉
Can i use gluten free flour?
You can substitute with gluten-free flour, however you will want to add a 1/2tsp-1 tsp of xantham gum so the muffins will rise properly and have the right texture!
I love using molasses when baking. These muffins look fantastic. Is it 1/3 cup molasses? The word “cup” is missing from the recipe.
One more question, if I don’t have coconut sugar, could I use the same amount of honey instead?
Hi Edwina! Yes it is cups. And you can replace coconut sugar with brown or white sugar, and honey as well! I believe honey may change the texture a bit-make them a bit more moist, but I’m sure they will turn out equally delicious!
Going to make these! But do you think I can take honey or maple syrup instead of molasses?
Hi Alexandra, yes of course! it will change the flavour slightly but work just as well!
Hi! Do you think I could use all purpose flour instead of spelt? Also does 1/3 molasses mean “1/3 cup”?
Hi Kiki, yes you can replace the spelt with any plain flour you like. and it is 1/3 cup molasses, it has been edited correctly in the recipe!