These fluffy apple blueberry muffins are perfect for a quick breakfast! Made with juicy blueberries and tart apples, these unique muffins are easy to make!

Apple Blueberry Muffins

I love blueberry muffins, and I’ve always enjoyed apple muffins so I started thinking, why not make a combination of my two favorite muffins? Sweet blueberries are the perfect combination with tart granny smith apple pieces. I’m always trying new healthy muffin recipes for my picky toddler and these were a winner. These fluffy muffins will quickly become a family favorite. 

Variations and Substitutions

  • If you want to make these with whole wheat flour, substitute one cup of all-purpose flour for white whole wheat flour. I don’t recommend substituting all of the flour for whole wheat as the muffins will become tough and dry.
  • ​You can use fresh or frozen blueberries. If using frozen berries, you do not need to thaw them.
  • I used 1% milk but 2% or whole milk works fine too. 

How to Make Apple Blueberry Muffins

Tips for Perfect Muffins

  • Prevent Soggy Bottoms: Toss the blueberries and apple chunks in a bit of flour before folding them into the muffin batter. This helps prevent them from sinking to the bottom of the muffin and distributes them evenly.
  • Uniform Size: Cut your apple chunks into uniform sizes so that they bake evenly within the muffins. This ensures that each bite has a balanced mix of flavors.
  • Fold Gently: When incorporating the blueberries into the batter, fold them in gently. Overmixing can lead to tough muffins, so just fold until combined.
  • Use Muffin Liners: To prevent sticking and make clean-up easier, use muffin liners or grease the muffin tin well. I like using silicone liners for a reusable option.
  • Divide Evenly: I like to use an ice cream scoop to easily divide the batter evenly in the muffin tray.
  • Cooling Time: Allow the muffins to cool in the pan for about 5 minutes before transferring them to a wire rack. This prevents them from becoming too soggy or falling apart.
  • Store Well: Store the muffins in an airtight container at room temperature for a day or two. If you plan to keep leftover muffins longer, store them in the freezer and reheat in the microwave.

​Other Muffin Recipes

If you enjoy these healthy muffins, try my blueberry banana muffins, pumpkin muffins, apple cinnamon muffins, or my lemon blueberry muffin recipe. If you’re gluten-free, try my almond flour muffins and if you’re looking for a vegan option, try my vegan blueberry muffins.

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Apple Blueberry Muffins

Apple Blueberry Muffins

  • Author: Liz Thomson
  • Prep Time: 15 minutes
  • Cook Time: 20 minutes
  • Total Time: 35 minutes
  • Yield: 12 muffins 1x
  • Category: Breakfast
  • Method: Oven
  • Cuisine: American
  • Diet: Vegetarian


These fluffy apple blueberry muffins are perfect for a quick breakfast! Made with juicy blueberries and tart apples, these unique muffins are easy to make!


Units Scale
  • 2 1/4 cups all-purpose flour
  • 1/2 cup brown sugar, packed
  • 1/2 cup granulated sugar
  • 2 teaspoons baking powder
  • 1 teaspoon ground cinnamon
  • 1/2 teaspoon salt
  • 1 1/2 cups fresh or frozen blueberries
  • 2 eggs
  • 3/4 cup low fat milk
  • 1/2 cup butter, melted and cooled
  • 1 teaspoon vanilla extract
  • 1 large Granny Smith apple, diced


  1. Preheat the oven to 375 degrees. Prepare a muffin tin with cupcake liners spritzed with nonstick cooking spray.
  2. In a large bowl, combine the flour, sugars, baking powder, cinnamon, and salt. Stir in the blueberries. Create a well in the center of the flour mixture and set it aside.
  3. In another bowl, whisk the eggs until foamy. Add the milk, melted butter, and vanilla, mixing until blended. Stir in the apple.
  4. Add the wet mixture to the flour mixture all at once. Stir just until the ingredients are moistened; the batter should be lumpy.
  5. Divide the batter evenly between the 12 prepared muffin cups, filling each one almost to the top.
  6. Bake for 20 to 24 minutes, or until the muffins turn golden and a wooden toothpick inserted into the centers comes out clean.

  7. Allow the muffins to cool in the muffin cups on a wire rack for 5 minutes. Then, remove them from the muffin cups and serve them warm.