Name: Apple Crumble Cupcakes Recipe
Prep time: 25 min
Cook time: 22 min
Total time: 60 min
Ingredients: 1 1/2 cups all-purpose flour; 1 teaspoon baking powder; 1/2 teaspoon baking soda; 1/2 teaspoon fine sea salt; 1 1/2 teaspoons ground cinnamon; 1/4 teaspoon ground nutmeg; 3/4 cup granulated sugar; 1/4 cup light brown sugar, packed; 1/2 cup unsalted butter, melted and slightly cooled; 2 large eggs, room temperature; 1 teaspoon pure vanilla extract; 1/2 cup plain Greek yogurt or sour cream; 1/4 cup milk (whole or 2%); 1 1/2 cups peeled, finely chopped apples; 1/2 cup all-purpose flour; 1/4 cup light brown sugar, packed; 2 tablespoons granulated sugar; 1/2 teaspoon ground cinnamon; 1/4 teaspoon fine sea salt; 4 tablespoons cold unsalted butter, cut in small cubes; 8 ounces cream cheese, softened; 1/2 cup unsalted butter, softened; 3 cups powdered sugar, sifted; 1 teaspoon pure vanilla extract; 1/2 teaspoon ground cinnamon; pinch fine sea salt; 1-2 tablespoons milk or cream, as needed for texture

Apple Crumble Cupcakes Recipe tastes like a cozy slice of apple pie tucked into a soft cinnamon cupcake with a crunchy, buttery topping. It works great for fall bake sales, holiday dessert tables, or any weeknight when you want a from-scratch treat in about 1 hour. I tested these for a school fundraiser and ended up “taste testing” three in a row, strictly for research purposes.

Why You Should Try This Apple Crumble Cupcakes Recipe

These apple crumble cupcakes pack three textures in one bite: tender spiced cake, juicy apple pockets, and a crisp, buttery streusel on top. You get all the flavors of apple crumble without juggling multiple pans or a pie crust.

The recipe uses simple pantry ingredients and fresh apples, so you skip fancy tools or specialty products. You can bake the cupcakes ahead, frost later, and still serve them soft and bakery-level good.

“These taste like a bakery apple crumble and a cupcake had the best possible baby, and I ate three before dinner. ★★★★★”

Ingredients You’ll Need

For the apple cupcakes

1 ½ cups all-purpose flour
1 teaspoon baking powder
½ teaspoon baking soda
½ teaspoon fine sea salt
1 ½ teaspoons ground cinnamon
¼ teaspoon ground nutmeg (freshly grated if you have it)
¾ cup granulated sugar
¼ cup light brown sugar, packed
½ cup unsalted butter, melted and slightly cooled
- Use real butter, not margarine, for better flavor.
2 large eggs, room temperature
1 teaspoon pure vanilla extract
- I like Nielsen-Massey or Costco vanilla for consistent flavor.
½ cup plain Greek yogurt or sour cream
- Either works; yogurt keeps the crumb a bit lighter.
¼ cup milk (whole or 2%)
1 ½ cups peeled, finely chopped apples
- Use firm apples like Granny Smith, Honeycrisp, or Pink Lady.
- If you only have softer apples, chop them smaller so they cook through.

For the crumble topping

½ cup all-purpose flour
¼ cup light brown sugar, packed
2 tablespoons granulated sugar
½ teaspoon ground cinnamon
¼ teaspoon fine sea salt
4 tablespoons cold unsalted butter, cut in small cubes
- Keep the butter cold so the crumble bakes up crisp, not greasy.

For the cinnamon cream cheese frosting

8 ounces cream cheese, softened
- Use full-fat brick style, not the tub.
½ cup unsalted butter, softened
3 cups powdered sugar, sifted
1 teaspoon pure vanilla extract
½ teaspoon ground cinnamon
Pinch of fine sea salt
1–2 tablespoons milk or cream, as needed for texture

Pantry shortcuts and substitutions

Use store-bought apple pie spice instead of separate cinnamon and nutmeg. Use 2 teaspoons in the batter and ½ teaspoon in the crumble.
Swap half the all-purpose flour with whole wheat pastry flour for a slightly heartier cupcake.
Use canned apple pie filling in a pinch: chop it very small, drain extra syrup, and fold in 1 cup instead of fresh apples.
If you prefer less frosting, cut the frosting ingredients in half.

Equipment list

12-cup muffin tin
Paper cupcake liners
Two medium mixing bowls and one large mixing bowl
Hand mixer or stand mixer with paddle attachment
Rubber spatula
Whisk
Measuring cups and spoons
Small cookie scoop or tablespoon for portioning batter
Cooling rack
Piping bag and tip (optional; you can also spread frosting with a knife)

Tips & Tricks

Use room temperature eggs, yogurt, and milk so the batter mixes smoothly and bakes evenly.
Chop apples very small, about pea-sized, so they soften fully and distribute through every bite.
Do not overmix the batter; stir just until no dry streaks of flour remain to keep cupcakes tender.
Fill cupcake liners about two-thirds full to prevent overflow under the crumble topping.
Chill the crumble in the fridge while you mix the batter so it stays firm and crisp in the oven.
Press the crumble very gently into the batter so it sticks but still keeps a rough, craggy texture.
Rotate the pan halfway through baking if your oven heats unevenly.
Let cupcakes cool completely before frosting or the cream cheese frosting will slide and melt.
Use a small offset spatula or piping bag to keep frosting neat around the crumble.
Taste your apples; if they taste very tart, add an extra tablespoon of sugar to the batter.

How to Make Apple Crumble Cupcakes Recipe

Step 1: Mix the crumble topping

Add flour, brown sugar, granulated sugar, cinnamon, and salt to a medium bowl and whisk to combine. Toss in the cold butter cubes and cut them in with your fingers or a pastry cutter until the mixture forms clumps and pea-sized bits. Place the bowl in the fridge while you prepare the cupcake batter so the crumble stays cold and firm.

Step 2: Prep the apples and dry ingredients

Peel, core, and finely chop the apples, then set them aside. In a medium bowl, whisk flour, baking powder, baking soda, salt, cinnamon, and nutmeg until everything looks evenly mixed. This step keeps the leavening and spices from clumping in the batter.

Step 3: Mix the wet ingredients

In a large bowl, whisk granulated sugar, brown sugar, and melted butter until the mixture looks smooth and slightly thick. Add eggs one at a time, whisking well after each addition, then stir in vanilla. Whisk in yogurt and milk until the mixture looks creamy and fully combined.

Step 4: Combine batter and fold in apples

Sprinkle the dry ingredients over the wet mixture and stir gently with a spatula until you see no dry flour. Fold in the chopped apples, scraping the bottom and sides of the bowl so apples spread evenly through the batter. Stop mixing as soon as everything looks combined so the cupcakes stay soft.

Step 5: Fill the pan and add crumble

Line a 12-cup muffin tin with paper liners. Divide the batter evenly between the cups, filling each about two-thirds full. Take the chilled crumble from the fridge and sprinkle a generous layer over each cupcake, lightly pressing it so it sticks on top.

Step 6: Bake the cupcakes

Place the muffin tin in a preheated 350°F (175°C) oven. Bake 18 to 22 minutes, until a toothpick inserted in the center of a cupcake comes out clean or with a few moist crumbs. Let the cupcakes cool in the pan 5 minutes, then move them to a wire rack and cool completely before frosting.

Step 7: Make the cinnamon cream cheese frosting

Beat softened cream cheese and butter in a large bowl with a hand mixer or stand mixer until the mixture looks smooth and fluffy, about 2 to 3 minutes. Add powdered sugar, vanilla, cinnamon, and salt, then mix on low until the sugar incorporates. Turn the speed to medium and beat until the frosting looks light and creamy, adding 1 to 2 tablespoons of milk or cream as needed for a spreadable texture.

Step 8: Frost and finish

Once the cupcakes cool completely, pipe or spread the cinnamon cream cheese frosting on top of the crumble. You can swirl the frosting in the center and leave some crumble peeking out around the edges for a rustic look. If you want extra flair, sprinkle a tiny pinch of cinnamon or a few extra crumble crumbs on top of the frosting.

What to Serve with Apple Crumble Cupcakes Recipe

Serve these apple crumble cupcakes slightly chilled or at room temperature with a cold glass of milk or a mug of hot apple cider. A simple vanilla or cinnamon yogurt on the side turns one cupcake into a cozy snack plate. Kids love them with hot chocolate, and adults can enjoy them with strong coffee or a chai latte. Add a scoop of vanilla ice cream next to a warm cupcake if you want full apple-pie energy without the pie plate.

Storage Options

Store frosted cupcakes in an airtight container in the fridge for up to 4 days; let them sit at room temperature 15 to 20 minutes before serving.
Keep unfrosted cupcakes at room temperature in an airtight container for up to 2 days, then move them to the fridge after that.
Freeze unfrosted cupcakes, tightly wrapped, for up to 2 months; thaw overnight in the fridge or at room temperature for about 1 hour.
Freeze leftover frosting in an airtight container for up to 1 month; thaw in the fridge, then re-whip with a splash of milk to smooth it out.
Refresh chilled cupcakes by letting them warm slightly on the counter or by heating an unfrosted cupcake in the microwave for 8 to 10 seconds before serving.