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stack of two healthy apple muffins sitting on wire cooling rack.

Healthy Whole Wheat Apple Muffins

5 Stars 4 Stars 3 Stars 2 Stars 1 Star 4.9 from 115 reviews
  • Author: Sally
  • Prep Time: 10 minutes
  • Cook Time: 22 minutes
  • Total Time: 35 minutes
  • Yield: 12 muffins
  • Category: Muffins
  • Method: Baking
  • Cuisine: American


These simple and healthy whole wheat apple muffins come together quickly. Feel free to skip the optional nuts and make sure to use shredded apple instead of chopped apple.


  • 2 cups (260g) whole wheat flour (spooned & leveled)
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • 2 teaspoons ground cinnamon
  • 1/2 teaspoon ground allspice
  • 1/2 teaspoon salt
  • 2 large eggs, at room temperature
  • 3/4 cup (133g) smooth unsweetened applesauce, at room temperature
  • 2/3 cup (160ml) pure maple syrup, at room temperature
  • 1/3 cup (70g) coconut oil, melted (or vegetable oil or melted butter)
  • 1 and 1/2 teaspoons pure vanilla extract
  • 2 cups (210g) shredded/grated apple (about 2 peeled apples)*
  • optional: 3/4 cup (about 90g) chopped pecans or walnuts
  • optional: 1 Tablespoon coarse sugar for sprinkling on top


  1. Preheat oven to 425°F (218°C). Spray a 12-count muffin pan with nonstick spray or line with cupcake liners. Set aside.
  2. In a large bowl, whisk the flour, baking powder, baking soda, cinnamon, allspice, and salt together until combined. Set aside. In a medium bowl, whisk the eggs, applesauce, maple syrup, oil, and vanilla together until combined. Pour the wet ingredients into the dry ingredients, stir a few times, and then add the shredded apple and pecans/walnuts. With a silicone spatula, fold everything together gently just until combined. The batter will be very thick.
  3. Spoon the batter into liners, filling them all the way to the top. If using, sprinkle tops evenly with coarse sugar. Bake for 5 minutes at 425°F, then, keeping the muffins in the oven, reduce the oven temperature to 350°F (177°C). Bake for an additional 16–18 minutes or until a toothpick inserted in the center comes out clean. The total time these muffins take in the oven is about 21–23 minutes. (For mini muffins, bake 11–14 minutes at 350°F (177°C).)
  4. Allow the muffins to cool for 5 minutes in the muffin pan, and then transfer to a wire rack to continue cooling, or enjoy warm.
  5. Muffins stay fresh covered at room temperature for a few days, then transfer to the refrigerator for up to 1 week.


  1. Freezing Instructions: For longer storage, freeze the muffins for up to 3 months. Thaw overnight in the refrigerator, then heat up in the microwave if desired.
  2. Special Tools (affiliate links): 12-count Muffin Pan | Cupcake Liners | Glass Mixing Bowls | Whisk | Box Grater | Silicone Spatula | Cooling Rack
  3. Whole Wheat Flour: If you don’t have whole wheat flour, you can replace with the same amount of all-purpose flour. My team and I have not tested this recipe with gluten-free flour, but here are some gluten-free blueberry muffins you might enjoy instead. (Feel free to replace blueberries with chopped apple.)
  4. Maple Syrup: For best results, use pure maple syrup, not breakfast syrup. The darker the pure maple syrup, the stronger the flavor. So if your maple syrup is extra dark with robust flavor, slightly reduce to 1/2 cup (120ml). If your maple syrup is golden or light amber colored (not very dark), use 2/3 cup as instructed. You can substitute honey if needed, but reduce the honey to 1/2 cup (170g).
  5. Shredded vs. Chopped Apples: It’s best to use shredded/grated apples in this muffin recipe because they work as a wet ingredient. I do not recommend chopping them instead. Feel free to peel the apples before shredding or leave the peels on—doesn’t matter either way.
  6. Why the initial high oven temperature? Like I do for most muffin recipes, bake the muffins for 5 minutes at a very hot temperature. Then, keeping the muffins in the oven, switch to a lower temperature for the remaining bake time. This initial high temperature will quickly lift the muffin tops so they’re extra high, then the centers will bake during the lower temperature bake time. This trick makes beautiful bakery-style muffins every time.
  7. Nutrition Information: Using SparkRecipes calculator, these muffins come out to 195 calories, 7.5g fat, 30g carbs each.