This post may contain affiliate links. Please read our disclosure policy.
These Healthy Applesauce Muffins are an easy one-bowl bake. Featuring whole wheat flour, warming spices, and coconut oil, they’re naturally sweetened with applesauce and honey for a wholesome breakfast, snack, or dessert.

When fall comes around, I love using apples in all sorts of recipes, especially homemade snacks for my kids. I always have a jar of applesauce in the pantry as it’s great for adding to muffin batters and quick breads. It creates a soft texture while adding fiber and natural sweetness to baked goods. These applesauce muffins always turn out so moist, with cozy flavors of cinnamon and nutmeg; they’re a hit with my whole family.
Recipe Overview
A Few Key Ingredients
Below are the key ingredients you’ll need to make Healthy Applesauce Muffins. You’ll find the full quantities in the recipe card further down the post.

Applesauce: Keeps the muffins moist and tender while adding natural sweetness. You can use store-bought applesauce or homemade applesauce; just make sure it’s unsweetened.
Eggs: Binds the batter, helping it achieve a fluffy texture. Use room-temperature eggs for the best results.
Natural sweetener: You can use either honey or maple syrup to enhance the muffins’ sweetness without refined sugar. Agave syrup or coconut sugar also work well here.
Coconut oil: Makes the muffins soft and moist. Melted butter or light olive oil also work well if preferred.
Flour: A mix of all-purpose and whole wheat flour forms the base of the batter, giving a light texture and added fiber. You can also substitute whole wheat flour with oat flour.
Spices: Cinnamon and nutmeg have a warming flavor that pairs well with the nutty whole-wheat flour and fruity applesauce.
Common Mistakes to Avoid
- Over-mixing the batter: Muffin batters can be easy to over-mix, which results in dense, gummy muffins. To prevent this, only fold the batter together until no floury streaks remain.
- Don’t use room-temperature ingredients: Always use room-temperature ingredients when baking, so the batter comes together correctly. If your eggs or applesauce are refrigerated, bring them to room temperature before using them in the recipe.
- Measuring flour incorrectly: When measuring flour using cups, it’s important to use the ‘spoon and sweep’ method to ensure you’re measuring out the correct amount. To do this: Fluff the flour in its container, then spoon it into the measuring cup (don’t tap or shake the cup) until it mounds above the rim. Use the back of a butter knife to sweep away the excess flour, back into its container.
- Not checking your oven’s temperature: Everyone’s ovens are slightly different (some run hotter, some colder), so it’s a good idea to check that your oven is preheated to the correct temperature. You can do this with a small oven thermometer placed inside the oven as it preheats. These are usually more reliable than your oven’s own temperature sensors and can tell you if you need to adjust the temperature up or down.

How to Make Healthy Applesauce Muffins
Before you start: Preheat the oven to 350°F and line a 12-cup muffin pan with liners or lightly grease it.
Step 1. In a large bowl, whisk together the applesauce, eggs, honey, oil, and vanilla.
Step 2. In a separate bowl, combine the flours, baking soda, baking powder, cinnamon, nutmeg, and salt.

Step 3. Add the dry ingredients to the wet ingredients and stir until just combined.
Step 4. Divide the batter evenly among the muffin cups.

Step 5. Bake for 18 to 22 minutes, or until a toothpick inserted into the center comes out clean.
Step 6. Allow the muffins to cool in the pan for 5 minutes before transferring to a wire rack.
Recipe Notes
Mix-ins: Fold a generous handful of mix-ins into the muffin batter for a boost of flavor and texture:
- Chopped walnuts or pecans
- Pumpkin seeds or sunflower seeds
- Chocolate chips
- Raisins or pitted, chopped dates
Storage: Store cooled muffins in an airtight container at room temperature for up to 3 days. Alternatively, individually wrap in plastic wrap then store in an airtight container in the freezer for up to 3 months. If frozen, thaw at room temperature before eating.

Questions I Get Asked a Lot
Sweetened applesauce will work in this recipe, but it can make the muffins taste too sweet. Unsweetened applesauce and honey already bring plenty of sweetness to the batter.
You can increase the whole wheat flour to 2 cups and omit the all-purpose flour for a higher-fiber muffin. The muffins will turn out slightly denser than the original recipe, though.
Yes, you can pour the batter into a lined 2lb loaf pan and bake at 350°F for 55-65 minutes, or until a toothpick inserted into the center comes out clean.
Yes, use a 1-to-1 gluten-free flour substitute that’s made for baking in place of the all-purpose and whole wheat flour in this recipe.
More Healthy Muffin Recipes
- Cinnamon Streusel Muffins
- Blueberry Banana Muffins
- Pumpkin Muffins
- Coffee Cake Muffins
- Greek Yogurt Chocolate Chip Muffins
- Orange Cranberry Muffins
- Strawberry Muffins
- Flourless Chocolate Muffins
Made these? Leave a comment below and let me know how it went. And tag me on Instagram so I can see your muffins!
Healthy Applesauce Muffins

Ingredients
- 1 cup unsweetened applesauce
- 2 large eggs
- ¼ cup honey or maple syrup
- ¼ cup melted coconut oil
- 1 teaspoon vanilla extract
- 1 cup whole wheat flour or oat flour
- 1 cup all-purpose flour
- 1/2 teaspoon baking soda
- 1 teaspoon baking powder
- 1 teaspoon ground cinnamon
- ¼ teaspoon nutmeg
- ¼ teaspoon salt
Instructions
- Preheat the oven to 350°F and line a 12-cup muffin pan with liners or lightly grease it.
- In a large bowl, whisk together the 1 cup unsweetened applesauce, 2 large eggs, ¼ cup honey or maple syrup, ¼ cup melted coconut oil, and 1 teaspoon vanilla extract.

- In a separate bowl, combine the 1 cup whole wheat flour or oat flour, 1 cup all-purpose flour, 1/2 teaspoon baking soda, 1 teaspoon baking powder, 1 teaspoon ground cinnamon, ¼ teaspoon nutmeg, and ¼ teaspoon salt.

- Add the dry ingredients to the wet ingredients and stir until just combined.

- Divide the batter evenly among the muffin cups.

- Bake for 18 to 22 minutes, or until a toothpick inserted into the center comes out clean.

- Allow the muffins to cool in the pan for 5 minutes before transferring to a wire rack.

Notes
- Storage: Store cooled muffins in an airtight container at room temperature for up to 3 days. Alternatively, individually wrap in plastic wrap, then store in an airtight container in the freezer for up to 3 months. If frozen, thaw at room temperature before eating.
- Use unsweetened applesauce so you can control the sweetness of the muffins.
- You can use whole wheat flour or oat flour in the recipe. Oat flour will give the muffins a softer, more tender texture.
- Don’t overmix the batter once you add the flour. Stir just until combined.
- You can add chocolate chips, chopped walnuts, pecans, or raisins if you want to change them up.
- Let the muffins cool in the pan for a few minutes before transferring them to a cooling rack.
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.






