Healthy Apple Muffins

These are the best healthy apple muffins because they are full of apple flavor, wholesome, and soft. They bake up wonderfully moist and with the perfect amount of sweetness. My kids love them and so will you.

healthy apple muffins baked with some split in half showing apple chunks.

Here’s Why These Are the BEST Healthy Apple Muffins

  • Full of apple flavor – by adding apple cider, applesauce, and cooked apples!
  • Easy to mixWhat is great about muffins and most all quick bread is they use the muffin mixing method, so no mixer is required. The muffin mixing method incorporates all the wet ingredients into the dry ingredients all at once. This method is used to create the desired texture of muffins, but it also helps you get your batter made with minimal mixing to avoid toughness.
  • Wholesome and healthy- by replacing white flour with whole wheat, replacing oil with applesauce, and sweetening with maple syrup.
  • Moist – Even though we are using 100% whole wheat flour, the key is a perfect mix of liquid to dry ingredients.
  • Great for an on-the-go snack or breakfast!

Key Ingredients & Why They Work

ingredients shown to make healthy apple muffins
  • Whole Wheat Flour: is made up of whole wheat kernel (endosperm, bran, and germ) and has a higher protein content than all-purpose providing more fiber, nutrients, and flavor than white flour.
  • Chopped Apples: By chopping the apples and then sautéing them with cinnamon and brown sugar provides more flavor and texture than plain shredded apples. It may be an extra step but it is worth it! I used granny smith apples as they hold their structure after the sauté and bake.
  • Eggs: This recipe used to call for 1 egg. Eggs add moisture and structure in baking and since there is a lot of other liquids to balance the wheat flour, one egg works.
  • Unsweetened Applesauce: Make sure you use unsweetened applesauce here as we are using maple syrup to sweeten these muffins.
  • Pure Maple Syrup: Pure maple syrup sweetens the muffins and adds some moisture. Pure maple syrup is made from maple tree sap that has been boiled down to reduce the water and concentrate the sugars. Those sugars are caramelized which provides the syrup’s rich color and flavor.
  • Apple Cider: I love apple cider and wanted to pump up the apple flavor and also helped add moisture to the mix. Do not substitute apple juice here.
  • Buttermilk: Buttermilk brings a pleasant tang while adding very little fat. It also helps to tenderize gluten, giving baked goods a softer texture and more body.

You also need butter, cinnamon, nutmeg, salt, baking soda, baking powder, and vanilla extract. 

This muffin batter comes together with simple kitchen tools including a couple of bowls, a whisk, a spatula, and a muffin pan. If you need a recommendation, this muffin pan works great especially since I don’t love using cupcake liners.

How to make Healthy Apple muffins

Melt 2 tablespoons butter in a 12-inch skillet over medium-high heat. Add apples, brown sugar, cinnamon, and salt. Cook, stirring often until moisture has completely evaporated and apples are well browned about 7-9 minutes. Remove pan from heat and let cool for 10 minutes.

Whisk whole wheat flour, baking powder, baking soda, nutmeg, salt, and the remaining 1 teaspoon of cinnamon together in a large bowl.

Whisk egg, applesauce, apple cider, buttermilk, maple syrup, and vanilla together in a separate bowl for about 30 seconds. Add cooled apples to the mixture.

two healthy apple muffins stacked with apples in the background.
healthy apple muffins sliced in half on a white plate.

Best Apples to Use

I love using Granny smith apples for their sweet-tart flavor and crisp texture. They hold up to the cooking and baking while maintaining their structure. I use a little brown sugar to counterbalance the tartness.

Healthy Apple Muffins: Helpful Tips

  • Don’t overbake your muffins! This can dry them out and make the surface too dark. Bake them just until a skewer inserted into the center comes out clean, or with just a few moist crumbs.
  • Use a large cookie scoop. The scoop pictured above is a number 16 like this one. It makes it so easy to transfer the batter into the tin.
  • Cook the apples. The key to building big apple flavor lies in the technique. Cooking chopped Granny Smith apples in butter with brown sugar and cinnamon concentrates the sweet apple flavor. I learned this trick from America’s Test Kitchen’s apple-cinnamon muffin recipe.
  • Mix thoroughly but do not over-mix. The wheat flour takes a little more elbow grease to get thoroughly mixed together as the flour gets caught up in air pockets.

Even More Muffin Recipes

If you make these healthy apple muffins, be sure to leave a comment and review then here on the blog! I love hearing from you and this helps others find the recipe too!

healthy apple muffins split in half with whole muffins with apple slices and whole apple.

Healthy apple muffins

Sarah Allison
These are the best healthy apple muffins because they are full of apple flavor, wholesome, and soft. They bake up wonderfully moist and with the perfect amount of sweetness. My kids love them and so will you.
5 from 1 vote
Prep Time 20 minutes
Cook Time 23 minutes
Total Time 48 minutes
Course Breakfast
Cuisine American
Servings 12

Equipment

Ingredients
  

Cooked Apples

  • 2 tablespoons unsalted butter
  • 2 apples peeled cored and cut into ¼ inch pieces (approximately 3 cups)
  • 2 tablespoons packed dark brown sugar
  • ½ teaspoon cinnamon
  • 1/4 teaspoon diamond crystal kosher salt

Muffin mix

  • 2 cups whole wheat flour (260 grams)
  • 1 ¼ teaspoons diamond crystal kosher salt
  • 1 teaspoon baking soda
  • 1 teaspoon baking powder
  • ½ teaspoon freshly ground nutmeg
  • 1 teaspoon cinnamon
  • 1 egg
  • cup applesauce (80 grams)
  • ½ cup apple cider (116 grams)
  • ¼ cup buttermilk (63 grams)
  • cup maple syrup (196 grams)
  • 2 teaspoons vanilla extract

Instructions
 

  • Adjust oven rack to upper-middle position and heat oven to 400 degrees. Spray 12-cup muffin tin generously with vegetable oil spray. or line with cupcake liners. Set aside.
  • Melt 2 tablespoons butter in a 12-inch skillet over medium-high heat. Add apples, dark brown sugar, cinnamon, and salt. Cook, stirring often until moisture has completely evaporated and apples are well browned about 7-9 minutes. Remove pan from heat and let cool for 10 minutes.
  • Whisk whole wheat flour, baking soda, baking powder, freshly ground nutmeg, salt, and the remaining 1 teaspoon of cinnamon together in a large bowl.
  • Whisk applesauce, apple cider, buttermilk, maple syrup, egg, and vanilla together in a separate bowl for about 30 seconds. Add cooled apples to the mixture.
  • Pour the wet ingredients into the dry ingredients. With a spatula fold everything together gently just until combined. The batter will be thick.
  • Spoon the batter into tin or liners filling them almost to the top. Bake for 14-16 minutes at 400°F until golden brown and a toothpick inserted in the center comes out with a few crumbs.
  • Let muffins cool in muffin tin on wire rack for 5-10 minutes. Remove muffins from tin to wire rack and let cool.

Notes

Muffins stay fresh covered at room temperature for a few days, then transfer to the refrigerator for up to 1 week.
Freezing Instructions: For longer storage, freeze the muffins for up to 3 months. Thaw overnight in the refrigerator and heat in the microwave if desired.  Or heat in the microwave from frozen for about 30 seconds. 

Nutrition

Calories: 126kcalCarbohydrates: 24gProtein: 4gFat: 2gSaturated Fat: 1gPolyunsaturated Fat: 1gMonounsaturated Fat: 1gTrans Fat: 0.002gCholesterol: 14mgSodium: 382mgPotassium: 152mgFiber: 3gSugar: 7gVitamin A: 49IUVitamin C: 2mgCalcium: 43mgIron: 1mg
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