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5 from 21 votes

Whole Wheat Apple Crumb Muffins

These soft and moist Whole Wheat Apple Crumb Muffins are filled with sweet apples and piled high with a brown sugar streusel topping! They are a healthier yet delicious fall treat perfect for breakfast or snacking. Plus they freeze beautifully and only take 10 minutes of hands-on time. 
Prep Time10 mins
Cook Time15 mins
Total Time25 mins
Course: Breakfast
Cuisine: American
Servings: 15 muffins
Calories: 419kcal



  • cups (270 g) whole wheat pastry flour
  • 1 cup (213 g) (213g) packed light or dark brown sugar
  • 1 tablespoon baking powder
  • ¼ teaspoon kosher salt
  • 2 teaspoons ground cinnamon
  • ¼ teaspoons ground nutmeg
  • cup (160 mL) vegetable oil
  • ½ cup + 2 tbsp (142 mL) milk
  • 2 large eggs room temperature
  • teaspoon vanilla extract
  • cups peeled, chopped apples about 2 medium apples

Crumb Topping

  • ½ cup (48 g) whole wheat pastry flour
  • 1/8 teaspoon kosher salt
  • ¼ cup (53 g) (53 g) packed light or dark brown sugar
  • 2 tablespoons granulated sugar
  • ½ teaspoon ground cinnamon
  • ¼ cup (1/2 stick, 57 g) unsalted butter melted

Vanilla Icing (optional)

  • 1 cup (120 g) confectioners sugar
  • 2-3 tablespoons milk or heavy cream
  • ½ teaspoons ground cinnamon
  • ½ teaspoon vanilla extract


  • Preheat and prepare pan. Preheat oven to 375oF. Line pan with paper muffin cups or grease the wells and top of pan with non-stick cooking spray. 
  • Make crumb topping. In a small bowl, combine flour, salt, brown sugar, granulated sugar and cinnamon. Work butter into mixture until crumbly. Set aside.
  • Combine dry ingredients. Whisk together the flour, brown sugar, baking powder, salt, and spices in a large bowl. Make a well in the center by pushing the dry ingredients to the side and creating a hole in the middle. 
  • Combine wet ingredients. In a second mixing bowl, whisk together oil, milk, eggs, and vanilla extract. 
  • Add wet to dry. Pour wet ingredients all at once into the well in the flour mixture. Mix quickly and lightly with a rubber spatula, but do not overbeat. The batter will be lumpy. Stir in apples. Divide the batter into the wells, filling each well.
  • Sprinkle on crumb topping.
  • Bake muffins. Bake for 25 minutes, or until golden and a toothpick inserted comes out clean. Allow to cool in the pan for 5 minutes, then transfer each muffin to a wire cooling rack to continue to cool. 
  • Make icing. In a small mixing bowl, stir together all icing ingredients. Adjust consistency if needed. Drizzle on cooled muffins. 


  • Measure your flour accurately. The best method is to use a kitchen scale and measure your flour in grams. If you don't have a scale, use a spoon to scoop the flour into the measuring cup, then level it off gently with a butter knife. For more details, read my post on How to Measure Flour Correctly. 
  • Don't overmix the batter. Once you add the wet ingredients to the dry, mix until everything is just combined. Don't worry if it is still lumpy. Overmixing can lead to tough muffins or cause tunneling, which is essentially large air pockets (holes) in the muffins. So no overmixing!  
  • Portion your muffins evenly. Nowadays they make awesome LARGE ice cream/cookie/muffin scoopers that are perfect for getting even sized muffins. 
  • Storage: Cool, then store in air-tight container at room temperature for 3-5 days. 
  • Freezing: Cool, then wrap individually in plastic wrap. Store in a zipper bag and freeze for up to 3 months. Thaw at room temperature or in the microwave with the gentle defrost setting. 
  • For less fat content: You can use half oil and half applesauce for less fat.
  • Best Apples: I use honeycrisp apples in this recipe because they are sweet, juicy, and don't break down too much while baking. They're perfect! But there are other apple options that could work well too. Check out my post on The Best Apples for Baking to find the best substitutes.
  • No liners? You can make the muffins without liners if you prefer. Just make sure to grease the inside AND TOP of the muffin tin very well before baking. The muffins will bake up around the edges and stick to to the top if it isn't greased well.
  • Flour substitution: You can use AP flour if you want for these muffins. I wouldn't recommend using 100% regular whole wheat flour as they might come out very heavy and dense. Regular whole wheat flour has a much higher protein content so it can result in a heavy muffin. If you don't have whole wheat pastry flour on hand but want to still make these whole wheat I would recommend using white whole wheat flour, which has a softer texture. Or try using half whole wheat flour and half AP flour.


Calories: 419kcal | Carbohydrates: 68g | Protein: 7g | Fat: 15g | Saturated Fat: 3g | Cholesterol: 34mg | Sodium: 61mg | Potassium: 289mg | Fiber: 5g | Sugar: 38g | Vitamin A: 153IU | Vitamin C: 1mg | Calcium: 88mg | Iron: 2mg