These apple cupcakes with cinnamon cream cheese frosting are warmly spiced and studded with grated apple for extra moisture. The cupcakes have a tender, springy crumb and are finished with a tangy, lightly sweet cinnamon cream cheese frosting — a perfect treat for apple season.
Updated August 2, 2022: new photos, clarified tips and a slightly adjusted recipe for more consistent results.
These apple cupcakes combine warm spices, brown sugar and grated apple for both flavor and moisture. Vanilla complements the apple and spices, giving a balanced, cozy flavor. The cinnamon cream cheese frosting is tangy and not overly sweet so it enhances the cupcakes without overwhelming them.
Making Apple Cupcakes
This recipe is made from scratch and is straightforward. Because it uses melted butter, the batter can be mixed by hand. Follow the steps below for the best results.
- Preheat the oven to 350°F (180°C; 170°C fan). Line a muffin pan with paper liners. This recipe makes about 12–14 cupcakes; you may need two pans.
- In a medium bowl, whisk together the all-purpose flour, baking powder, baking soda, cinnamon, nutmeg, ground cloves and salt. The spice blend is what complements the apple flavor.
- In a larger bowl, whisk the melted (and slightly cooled) butter with the brown sugar, granulated sugar, eggs, vanilla and milk. Use room temperature eggs and milk so the melted butter won’t scramble the eggs.
- Gently whisk the dry ingredients into the wet ingredients until the batter is smooth and you no longer see lumps. Stop mixing as soon as the ingredients are combined — overmixing can make cupcakes tough.
- Peel and grate the apples, then fold the grated apple into the batter until evenly distributed.
- Spoon the batter into the prepared liners, filling each about two-thirds to three-quarters full.
- Bake for 18–22 minutes, or until a toothpick inserted in the center comes out clean and the tops are set. Allow the cupcakes to cool in the pan for at least 15 minutes, then transfer to a wire rack to cool completely before frosting.
The Perfect Cinnamon Cream Cheese Frosting
The frosting is creamy, mildly tangy and balanced with cinnamon. You can adjust the sweetness by adding more or less powdered sugar, but the cream cheese provides flavor depth beyond sweetness alone. The cinnamon ties the frosting to the spiced apple cupcakes.
Important: use full-fat, brick-style cream cheese (not low-fat, spreadable or tub-style). These lower-fat, softer varieties are too loose to make a stable frosting.
If you prefer, caramel frosting with a drizzle of salted caramel is a delicious alternative to cream cheese frosting.
Choosing the Best Type of Apple
Many apple varieties work well here. I prefer Gala, Honeycrisp, Ambrosia or Pink Lady for their sweet, crisp texture. Granny Smith gives a pleasant tart contrast or you can combine a sweet and a tart apple. Avoid Red Delicious and Macintosh for baking; their texture and flavor don’t hold up well. You’ll need about 1½ cups grated apple — roughly two large apples. 
These apple cupcakes are moist, warmly spiced and perfectly finished with a cinnamon cream cheese frosting. They’re a lovely way to celebrate apple season and make a cozy dessert or snack.
Apple Cupcakes with Cream Cheese Frosting
Equipment
- 12-cavity muffin pan
Ingredients
Apple Cupcakes
- 1½ cups all-purpose flour (188 g)
- ½ teaspoon baking soda
- ½ teaspoon baking powder
- ¼ teaspoon salt
- 1½ teaspoons cinnamon
- ¼ teaspoon ground nutmeg
- ¼ teaspoon ground cloves
- ½ cup unsalted butter (112 g), melted and cooled slightly
- ½ cup brown sugar (100 g)
- ½ cup white sugar (100 g)
- 2 teaspoons vanilla extract
- 2 large eggs, room temperature
- 1/3 cup milk (80 ml), 2% recommended
- 1½ cups grated apple (peel apples first)
Cream Cheese Frosting
- 2/3 cup unsalted butter (150 g), softened
- 4 oz brick-style cream cheese (112 g)
- 2–3 cups powdered sugar (220–330 g), to taste
- 1 teaspoon vanilla extract
- ½ teaspoon cinnamon, or to taste
- ¼ teaspoon salt
- 1 tablespoon heavy cream, as needed
Instructions
Apple Cupcakes
- Preheat oven to 350°F (180°C; 170°C fan) and line muffin pans with liners.
- Whisk together flour, baking soda, baking powder, cinnamon, nutmeg, cloves and salt.
- In a separate bowl, whisk melted butter with both sugars, eggs, vanilla and milk until smooth and no sugar lumps remain.
- Gently whisk the dry ingredients into the wet until just combined.
- Fold in the grated apple until evenly mixed.
- Fill liners about 3/4 full. Bake one tray at a time in the center of the oven for 18–22 minutes, or until a toothpick comes out clean.
- Cool cupcakes in the pan 15 minutes, then transfer to a rack to cool completely before frosting.
Cream Cheese Frosting
- Beat the softened butter until smooth.
- Add the cream cheese in chunks and beat until just combined.
- Add 1 cup powdered sugar, vanilla, cinnamon and salt on low speed until combined.
- Beat in remaining powdered sugar ½–1 cup at a time until desired sweetness and consistency are reached. If frosting is too thick, add up to 1 tablespoon heavy cream.
- Pipe or spread on cooled cupcakes. Optionally garnish with a light dusting of cinnamon or thin apple slices right before serving to prevent browning.
Notes
- Milk: 1%, 2% or whole milk all work well. Avoid skim.
- Apples: Use Gala, Honeycrisp, Pink Lady or Ambrosia for best texture and flavor. Granny Smith adds tartness. Avoid McIntosh and Red Delicious.
- Cream Cheese: Use full-fat, brick-style cream cheese for stable frosting.
- Storage: Store frosted cupcakes in an airtight container at room temperature up to 8 hours or refrigerated up to 4 days. They’re best fresh.
- Make Ahead: Bake and cool cupcakes a day ahead, store at room temperature in an airtight container, and frost the next day.
- Nutrition: Estimates are based on one cupcake with frosting, assuming 12 equal cupcakes and all frosting used.
Nutrition
Estimated per cupcake: Calories 491 kcal; Carbohydrates 75 g; Protein 3 g; Fat 21 g; Saturated Fat 13 g; Sugar 63 g; Sodium 166 mg.