If you’re looking for a healthy snack to enjoy this season, try our whole wheat apple muffins. These desserts are moist, flavorful, and full of apple goodness. Whether for breakfast, a snack, or even dessert, these muffins are always a hit.
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Whole Wheat Apple Muffins Recipe
Whole wheat apple muffins are a delicious and nutritious snack. They offer a heartier texture and richer, nuttier flavor compared to muffins with all-purpose flour. The whole wheat flour gives them a hearty texture and a boost of fiber, while the apples add natural sweetness and moisture. Spices like cinnamon bring a gentle warmth, making them an ideal fall treat.

These muffins are incredibly easy to prepare, requiring just a few simple steps and pantry staples. They’re perfect for breakfast, a snack, or a light dessert. I often enjoy one when I need a burst of wholesome energy or something sweet that won’t weigh me down.
These treats pair well with Greek yogurt, a smear of almond or peanut butter, or a slice of sharp cheddar cheese. For a cozier treat, they can be served with warm apple cider, chai tea, or a cup of spiced coffee.
You can enjoy these whole wheat apple muffins with a simple fruit salad, creamy cottage cheese, or a handful of walnuts for added crunch. For breakfast, they work beautifully alongside scrambled eggs or a smoothie bowl.
Here’s how to make the whole wheat apple muffins:

Whole Wheat Apple Muffins
Nutrition
Ingredients
- 1 ½ cups whole wheat flour
- ½ cup rolled oats
- 1 ½ tsp baking powder
- ½ tsp baking soda
- ½ tsp salt
- 1 tsp ground cinnamon
- ¼ tsp ground nutmeg
- 2 large eggs
- ½ cup maple syrup or honey
- ½ cup unsweetened applesauce
- ⅓ cup neutral oil like canola or vegetable
- 1 tsp vanilla extract
- 1 ½ cups peeled, diced apples about 2 medium apples
- ¼ cup chopped walnuts or raisins Optional
Instructions
- Preheat oven to 350°F (175°C). Line or grease a 12-cup muffin tin.
- In a large bowl, whisk together flour, oats, baking powder, baking soda, salt, cinnamon, and nutmeg.
- In another bowl, beat the eggs. Stir in maple syrup, applesauce, oil, and vanilla.
- Add the wet ingredients to the dry and mix gently until just combined.
- Fold in the diced apples (and nuts or raisins if using).
- Spoon the batter evenly into muffin cups, filling about ¾ full.
- Bake for 20–22 minutes or until a toothpick comes out clean.
- Let cool in the pan for 5 minutes, then transfer to a wire rack.
Notes
- Use sweet apples like Fuji or Honeycrisp for natural sweetness.
- Wrap the muffins individually and freeze up to 2 months.
- Use flax eggs and plant-based yogurt instead of eggs/applesauce for vegan version.
- For crunch, top with a sprinkle of oats or brown sugar before baking.
Whole Wheat Apple Muffins Variations
Here are some variations and creative twists on classic whole wheat apple muffins:
- Nutty Apple Muffins include chopped walnuts or pecans for extra crunch and healthy fats.
- Vegan Versions use flaxseed meal mixed with water instead of eggs, along with plant-based milk and oil.
- Gluten-Free Muffins swap out the whole wheat flour for a gluten-free flour blend.
- Carrot-Apple Muffins blend shredded carrot into the batter. This adds sweetness and vibrant color, plus a nutritional boost.

- Apple Raisin Muffins incorporate sweet, chewy raisins for extra bursts of flavor and natural sweetness in every bite.
- Apple Oat Muffins add rolled oats to the batter for a slightly heartier texture and more sustained energy release.
- Spiced Chai Apple Muffins include ground ginger, nutmeg, and allspice alongside cinnamon. This version delivers a deeper, more aromatic flavor profile.
- Streusel-Topped Apple Muffins are crowned with a crumbly brown sugar-butter topping. This adds an indulgent, bakery-style finish without making the muffins overly sweet.
I love how whole wheat apple muffins make healthy snacking so enjoyable. With so many easy variations to try, there’s always a new twist to keep things interesting. Whether you enjoy them with your morning coffee, as an after-school treat, or tucked into a lunchbox, these muffins are a cozy, wholesome way to celebrate the flavors of fall.