Made with whole wheat flour, sweetened with honey, and kept light and moist with tons of applesauce, these healthy Applesauce Muffins are bursting with delicious apple cinnamon flavor!

Tender, light, and loaded with apple flavor, these Apple Cinnamon Muffins are the perfect fall treat.
They are filled with warm spices, notes of apples, and have the texture of a cake. In fact, they remind me of the flavor and texture of an apple cider donut--even down to the cinnamon-sugar coating.
While these muffins taste like a decadent treat, they are actually quite a wholesome snack. Made with whole wheat flour, sweetened naturally with applesauce and honey (except for the sprinkling of sugar on top), these healthy muffins are wholesome enough to enjoy anytime. Paired with a hot cup of coffee or a glass of Mulled Cider, I can not think of a better muffin to enjoy on crisp fall mornings.
Notes on Ingredients Needed
- Whole Wheat Flour--Whole wheat flour, white wheat flour, and all-purpose flour all work equally well in these muffins. In fact, I have even made Gluten-Free Applesauce Muffins using 1:1 Gluten-Free Flour Blend.
- Nutmeg--Freshly grated nutmeg is a must for optimum flavor. Nutmeg lasts forever in your pantry and is SO much tastier than ground nutmeg.
- Honey--Feel free to use maple syrup in place of honey.
- Applesauce--Use unsweetened applesauce--homemade applesauce, instant pot applesauce or store-bought applesauce are all fine.
- Oil--Canola oil or melted and cooled butter or coconut oil all work well.
- Eggs--I have had success using flax eggs to make Egg-Free Applesauce Muffins.
- Cinnamon Sugar--I love to top these muffins with a combination of cinnamon and sugar. This is totally optional but adds an irresistible crunchy, sugary sweet topping.
How to Make Applesauce Muffins
- Sift or whisk together flour, baking soda, baking powder, salt, cinnamon, and nutmeg until well combined.
- In a separate bowl, mix together applesauce, honey, oil, eggs, and vanilla.
- Add wet ingredients to dry ingredients and mix until just combined.

- Using an ice cream scoop or ¼ cup measuring cup, measure out muffin batter a greased or lined muffin tin.
- Mix together reserved cinnamon and sugar together and then sprinkle ¼ teaspoon of mixture over each muffin.

- Bake Applesauce Muffins until a toothpick inserted into the center comes out clean.
- Place muffin tin on a cooling rack and cool muffins in muffin tin for 10-15 minutes.
- Remove muffins from the muffin tin and finish cooling completely on a cooling rack.

Storing Applesauce Muffins
Because these healthy muffins have no preservatives and are whole wheat, they will likely begin to grow mold if left at room temperature for more than 24 hours. It is best to allow the muffins to cool completely and then store them in a sealed container in the fridge for 3-5 days.
Alternatively, you can freeze applesauce muffins. To do so, place the cooled muffins on a cookie sheet and freeze for 30-60 minutes until solid. This process helps muffins not stick together when placed in a container in the freezer. Once frozen solid, place the muffins into a freezer-safe bag and store them in the freezer for up to 3 months. Defrost in the fridge overnight, or warm in the microwave for 1-2 minutes to heat before serving.
More Healthy Muffin Recipes
- Healthy Blueberry Muffins
- Peanut Butter Banana Muffins
- Healthy Chocolate Zucchini Muffins
- Healthy Carrot Cake Muffins
- Healthy Chocolate Chip Muffins
- Whole Wheat Cornbread Muffins
If you enjoyed these Applesauce Muffins, please be sure to leave a comment and review below.

Applesauce Muffins
Ingredients
- ¾ cup unsweetened applesauce
- ⅔ cup honey
- 2 eggs
- ⅓ cup canola oil
- 1 teaspoon vanilla extract
- 2 cups whole wheat flour
- ¼ teaspoon baking powder
- ½ teaspoon baking soda
- 3 teaspoons cinnamon divided
- ½ teaspoon nutmeg freshly grated
- ½ teaspoon salt
- 1 tablespoon sugar
Instructions
- Preheat the oven to 350 degrees Lightly grease 10 wells in a standard 12-cup muffin tin with nonstick spray or line with silicone liners.
- In a large bowl, sift together the flour, baking powder, baking soda, 2 teaspoons cinnamon, and salt. Freshly grate nutmeg into the dry ingredients. Whisk together to combine evenly.
- In a separate bowl, mix together the applesauce, honey, eggs, oil, and vanilla.
- Add the wet ingredients into the flour mixture. Stir until just combined.
- Evenly divide the batter between the prepared muffin pan, each muffin cup holds about ¼ cup of batter.
- Combine the remaining teaspoon of cinnamon with the sugar. Sprinkle ½ teaspoon over each muffin.
- Bake for 18-20 minutes or until a toothpick inserted into the center comes out clean.
- Cool the muffins on a cooling rack for 10 minutes and then remove from the muffin tin and cool completely.
- Store the cooled muffins in a sealed container at room temperature for 24 hours, or in the fridge for 3-4 days.
Judy Evans
Yum! I made Winesap applesauce yesterday... Used it in these muffins today. Wonderful! I must stop eating them!! The only modification I made was not reading the instructions that the sugar went on top ... Used a bit of Maple sugar, which went in instead of on... Lol. Thank you for this recipe! I plan to try a bit of orange or lemon zest in a future batch, maybe pecans another time. A wonderful recipe on it's own, but also seems to be a good base for additions.
Barb Walker
I made these to go with roast pork for dinner. I'm gluten free so I swapped almond flour and GF flour for the whole wheat. I ran out of honey and used some honey, some maple syrup. Tossed in raisins and chopped walnuts. They are fantastic! So moist and flavorful!
Kristen Chidsey
Thanks for sharing your modifications and I am so glad you enjoyed.
Kalee
These applesauce muffins are a family staple! They are so yummy, sweet and moist!!
Kristen Chidsey
I love hearing that your family enjoys these as much as mine😊
Claudia Lamascolo
The smell alone of these muffins was magnificent while baking no less slathered with butter! yummy
Kristen Chidsey
These muffins do smell quite amazing with baking! So glad you enjoyed.