November 28, 2022


Cooking Is My World

Healthy Applesauce Muffins | A Mind “Full” Mom

These Applesauce Muffins are light, tender, and bursting with warming spices. Made with whole wheat flour, sweetened with honey, and made with less oil than most muffins, this easy recipe for Applesauce Muffins makes the perfect healthy treat.

Applesauce Muffin next to fresh apples and blue napkin.

Tender, light, and loaded with apple flavor, Applesauce Muffins have the taste and texture of a spice cake, yet are secretly healthy.

I say secretly healthy, not because there is anything secret about the recipe. They just taste so incredibly decadent, that it is hard to believe they are actually good for you!

Yet these Applesauce muffins are made with incredibly wholesome ingredients.

  • The refined flour has been swaped out for whole wheat flour, making these muffins full of whole grains.
  • Honey and applesauce both with to sweeten the muffins without the need to add any refined sugars to the muffin batter.
  • Not only does the applesauce work to sweeten and flavor these muffins, but it also significantly reduces the amount of oil added to the batter, keeping these muffins lower in fat, yet incredibly moist and tender.
  • This recipe for applesauce muffins is made without milk or butter, keeping the muffins completely dairy-free!

These applesauce muffins make the perfect wholesome treat fit for any time of the day, especially when paired with a homemade latte or a glass of mulled cider. YUM!

Notes on Ingredients Needed

Ingredients labeled on counter for applesauce muffin recipe.
  • Whole Wheat Flour: This recipe has been created using 100% whole wheat flour to create a light muffin that is still full of whole grains. You can opt to use whole white wheat flour, or all-purpose flour in place of the whole wheat flour if desired.
  • Honey: While this recipe calls for honey, you can use swap it out for 100% maple syrup. Either option makes a delicious natural sweetener for these muffins.
  • Applesauce: To keep these muffins refined sugar-free, be sure to use unsweetened applesauce. Either 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 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

  • To combine your dry ingredients, I do recommend sifting the flour, baking soda, baking powder, salt, cinnamon, and nutmeg together. This will help to ensure there are no lumps or clump in your muffin matter. If you don’t opt to sift the ingredients, be sure to whisk them really well to break up any lumps of baking soda and/or baking powder.
  • In a separate bowl, mix together applesauce, honey, oil, eggs, and vanilla until the eggs are fully broken down and everything is nice and combined together.
  • Add wet ingredients to dry ingredients and fold the batter together 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.
Applesauce Muffin Batter in Clear Bowl Next to muffin tin and eggs.
  • Evenly scoop out the muffin batter into a greased or lined muffin tin. 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 exact same size, which means they will bake evenly.
  • To finish the muffins, mix together a bit of granulated sugar with cinnamon and sprinkle over the top of each muffin. This is an optional step, so feel free to skip this step if you don’t want to add any refined sugar to the muffins.
Sprinkling cinnamon sugar on muffin batter.
  • Bake the applesauce muffins until a toothpick inserted into the center comes out clean and then cool the muffins in the muffin tin a cooling rack for 10-15 minutes.
Muffin Tin with Baked Applesauce Muffins with cinnamon sugar coating.
  • Remove muffins from the muffin tin and finish cooling completely on a cooling rack.
Applesauce Muffin on cooling rack.

Storage Instructions

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 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.

Dietary Modifications

I have tested this recipe out using all of the following modifications, to ensure you can have delicious results!

  • 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 flax eggs.

More Healthy Muffin Recipes

If you enjoyed these Applesauce Muffins, please be sure to leave a comment and review below.

Applesauce muffin next to apples and cinnamon stick

Applesauce Muffins

These Healthy Applesauce Muffins are made with whole wheat flour, naturally sweetened, and kept light and moist with tons of applesauce.


Course: Bread

Cuisine: American

Prep Time: 10 minutes

Cook Time: 20 minutes

Total Time: 30 minutes

Servings: 10

Calories: 223kcal

Prevents your screen from going dark while preparing the recipe.


  • Preheat the oven to 350 degrees F. 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 the whole nutmeg into the dry ingredients. 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 into 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. 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.


Flour: Feel free to use all-purpose flour or a 1:1 gluten-free all-purpose flour in place of whole wheat flour.
Honey: Feel free to use maple syrup in place of the honey. 
Flax Eggs: In place of the eggs, mix together ⅓ cup of water with 2 tablespoons of ground flaxseed and let sit for 5 minutes. 
For VEGAN muffins: Use maple syrup in place of honey and flax eggs for eggs. 
Nutmeg: Freshly grated nutmeg is best. If using ground nutmeg, only use ⅛ teaspoon, as it can be overwhelming. 


Calories: 223kcal | Carbohydrates: 34g | Protein: 4g | Fat: 9g | Saturated Fat: 1g | Cholesterol: 33mg | Sodium: 177mg | Potassium: 139mg | Fiber: 4g | Sugar: 15g | Vitamin A: 53IU | Vitamin C: 1mg | Calcium: 33mg | Iron: 1mg

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This post was originally shared in 2019 but updated in 2022 with a new video.