Tender, light, and loaded with apple flavor, these Healthy Applesauce Muffins are reminiscent of a decadent spice cake, yet are made with wholesome ingredients.
Pair one of these delightful applesauce muffins with a mug of mulled cider or a Homemade Pumpkin Spice Latte and enjoy a cozy treat filled with warming fall flavors.

I don't know about your kids, but my kids are ALWAYS hungry! And because snacking is crucial for their growing bodies, I am always on a mission to find kid-friendly healthy snacks. And anyone looking for a snack for kids (or themselves) that isn't loaded with refined sugars, refined flour, and preservatives, knows that can be a challenge.
That is why you (and your picky kids) are going to LOVE these Applesauce Muffins. Just like my recipe for Oatmeal Chocolate Chip Muffins and Peanut Butter Banana Muffins, these muffins taste like a dessert, yet are made with whole grains, naturally sweetened, and 100% picky eater-approved.
what makes these applesauce muffins the best
- Amazing Flavor. Applesauce muffins are filled with warming spices and a sweet apple flavor to deliver a muffin that is simply delicious.
- Tender & Fluffy, Yet 100% Whole Grain. These applesauce muffins are made with whole wheat flour, yet these muffins are super soft and tender.
- Low in Fat & Refined Sugar. This applesauce muffin recipe uses applesauce which works to not only flavor the muffin but helps to naturally sweeten the muffin and reduce the amount of oil needed to keep the muffins moist.
- Wholesome Snack. Even though these applesauce muffins taste incredibly decadent, they are packed with whole grains and fiber, and lower in sugar than most muffins.
- Irresistible Cinnamon Sugar Coating. Just like my recipe for Cinnamon Baked Donuts, this healthier baked good gets a small amount of cinnamon sugar to make these muffins undeniably good.
- Dairy-Free.This recipe for applesauce muffins is made without milk or butter, making this muffin recipe great for anyone, even those with dairy allergies or intolerances.
Notes on Ingredients Needed

- Whole Wheat Flour: This recipe has been created using 100% whole wheat flour to create a light muffin that is full of whole grains. However, feel free to use whole white wheat flour or all-purpose flour if desired.
- Honey: While this recipe calls for honey, you can swap it out for 100% maple syrup. Either option makes a delicious natural sweetener and pairs well with the apple flavor in these muffins.
- Applesauce: To keep these muffins refined sugar-free, be sure to use unsweetened applesauce. Homemade applesauce, instant pot applesauce, or store-bought applesauce work.
- Oil: While this recipe does use less oil than most muffin recipes, you do need a bit of oil to keep the muffin tender. Use canola oil or melted and cooled coconut oil.
- Nutmeg: Instead of using ground nutmeg, use whole nutmeg and grate it yourself using a Microplane for optimum flavor. Nutmeg lasts forever in your pantry and is SO much tastier than ground nutmeg.
- Cinnamon Sugar: I love to top these applesauce muffins with a combination of cinnamon and sugar. This is optional but does add an irresistible crunchy, sugary sweet topping.
Dietary Modifications & Substitutions
I have tested this recipe out using all of the following modifications, to ensure you can have delicious results regardless of your dietary needs.
- Egg-Free Applesauce Muffins: Replace the eggs with flax eggs by combining ⅓ cup of water with 2 tablespoons of ground flaxseed. Let that mixture sit for 5 minutes and then add to the batter when the recipe calls for eggs.
- Gluten-Free Applesauce Muffins: Replace the whole wheat flour with a 1:1 gluten-free all-purpose flour blend.
- Vegan-Friendly Applesauce Muffins: In place of the honey, use maple syrup and replace the eggs with 2 tablespoons of ground flax seed mixed with ⅓ cup of water.
Tips for Making Applesauce Muffins
This recipe for applesauce muffins comes together easily and you will find the detailed instructions in the recipe card. However, I do want to walk you through a few expert tips to ensure that your muffins turn out fluffy, moist, and delicious.
Tip #1: Sift dry ingredients together. To combine your dry ingredients, I recommend sifting the flour, baking soda, baking powder, salt, cinnamon, and nutmeg, as this will help to ensure there are no lumps or clumps in your muffin matter. If you don't opt to sift the ingredients, be sure to whisk them well to break up any lumps of baking soda and/or baking powder.
Tip #2 Don't over-mix the batter. Fold the batter together using a spatula or wooden spoon, until no pockets of flour remain. Just keep in mind to not overmix your muffin batter, as this activates the gluten in the flour, and will cause your muffins to be tough.

Tip #3: Evenly divide the muffin batter. I have found that it is best to use an ice cream scoop or ¼ cup measuring cup to scoop out the batter. This keeps each muffin the same size, which means they will bake evenly.
Tip #4: Top with cinnamon sugar. This is an optional step and does add refined sugar to the recipe, but topping each muffin with a bit of cinnamon sugar to each muffin before baking adds an irresistible flavor and slightly caramelized muffin top.

Tip #5. Bake until just set. Bake the applesauce muffins until a toothpick inserted into the center comes out clean. I suggest checking the applesauce muffins after the lowest suggested cooking time and continuing to bake if needed. You don't want to overbake the muffins, or they can become tough and dry out.

How to Store Applesauce Muffins
Because these applesauce muffins have no preservatives and are made with 100% whole wheat flour, they will likely begin to grow mold if left at room temperature for more than 2 days. hours. It is best to allow the muffins to cool completely and then store them in a sealed container in the fridge for up to 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 Favorite Muffin Recipes
- Healthy Blueberry Muffins
- Pumpkin Banana Muffins
- Peanut Butter Banana Muffins
- Cranberry Orange Muffins
- Chocolate Zucchini Muffins
- Healthy Carrot Cake Muffins
- Oatmeal Chocolate Chip 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 large eggs
- ⅓ cup canola oil
- 1 teaspoon vanilla extract
- 2 cups whole wheat flour
- ¼ teaspoon baking powder
- ½ teaspoon baking soda
- 3 teaspoons ground cinnamon divided
- ½ teaspoon whole nutmeg grated on Mircoplane
- ½ teaspoon salt
- 1 tablespoon granulated sugar
Instructions
- Preheat the oven to 350 ℉. Lightly grease 10 wells in a standard 12-cup muffin tin with nonstick spray or line with silicone liners. Add 1 tablespoon of water to the empty muffin cups.
- In a large bowl, sift together the flour, baking powder, baking soda, 2 teaspoons of cinnamon, nutmeg, and salt. Whisk together to combine evenly.
- In a separate bowl, mix together the applesauce, honey, eggs, oil, and vanilla until well combined.
- Add the wet ingredients to the flour mixture. Fold the wet ingredients into the dry ingredients 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 in a small bowl. Sprinkle ½ teaspoon of the cinnamon sugar mixture 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.
Jo
What’s the water I’m the muffin liner do?
Kristen Chidsey
I recommend doing this to help prevent damage to the empty muffin tin and to add moisture to the oven.
Hannah
Can you added chopped apples to this recipe or would that mess up the baking time/consistency?
Kristen Chidsey
Hi Hannah! Without experimentation, I would hedge not a good idea, as it could mess up the consistency
Karen
I made these with coconut oil, maple syrup and all purpose flour. They were not overly sweet and so delish!
Kristen Chidsey
Thank you for sharing, Karen! I am thrilled to hear you enjoyed
Simone
Made these last minute when we had company. They smelled amazing and looked wonderful. They were a hit and I really like that the muffins are a little bigger. Used refined coconut oil, but otherwise followed recipe.
I don’t quite have enough apple sauce today, so I’m going to try to substitute pumpkin purée. It’s that time of year! Really hoping they come out, as I’ll be bringing them to brunch. Thanks for this recipe!
Kristen Chidsey
Hi Simone! I love hearing you enjoyed the applesauce muffins. You may love using my recipe for Pumpkin Muffins, which calls for both applesauce and pumpkin puree and uses coconut oil. However, just using a bit of pumpkin to replace the applesauce will work just as well!
Simone
I used pumpkin and brown sugar because I was out of liquid sweetener. Also used pumpkin pie spice. I don’t recommend these changes. The original recipe is great, but my swaps made for bland, dense muffins.
Kristen Chidsey
Thanks for sharing, Simone. Brown sugar would cause the biggest change in the texture of the muffins. The recipe accounts for liquid from the honey or maple syrup.
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.