These apple-cinnamon muffins are packed with huge apple flavor thanks to apple cider and chopped, cooked apples, with a fabulous cinnamon-sugar crunch on top. You’ll want to make an extra batch or two to keep in the freezer!

Basket of apple muffins with one broken in half.

Aside from the robust apple flavor, the topping on these muffins is absolutely TO DIE FOR… a combination of granulated and brown sugar, along with cinnamon – it’s a wonderfully sweet, crunchy coating and will make you want to save the top for last (at least, I did!).

Whether you go apple picking at a local orchard or just grab your favorites from the grocery store, these apple-cinnamon muffins NEED to go on your fall baking list. They’re not as quick to come together as most, but they are well worth every single second of prep time. We are obsessed with them!

Ingredients for apple muffins prepped in bowls on counter.

How to make them from scratch

This recipe is a little bit of an exception to quick one-bowl muffin recipes since you cook the apples down with some butter and brown sugar first, but it is 100% worth the extra time. This is how we make them:

  1. Cook the apples with butter, brown sugar, and cinnamon until the moisture has evaporated. Set aside to cool.
  2. Prep the pan.
  3. Whisk together the dry ingredients.
  4. Whisk the wet ingredients.
  5. Add the apple cider, yogurt, and vanilla to the wet ingredients.
  6. Fold the wet ingredients and cooked apples with the dry ingredients.
  7. Divide between the muffin cups.
  8. Sprinkle with the cinnamon-sugar topping.
  9. Bake until golden brown and there are a few moist crumbs on a toothpick.

Chopped apples cooked in a skillet.

Prepping the apples

The Best Apples to Use

The types of apples most preferred for baking need to be firm enough to hold their shape during the baking process and not turn to mush. While Granny Smith is a natural first choice, all of these other apples are fantastic (and delicious!) substitutes:

  • Honeycrisp
  • Jonagold
  • Golden Delicious
  • Pink Lady
  • Braeburn
  • Cortland

Chopped vs shredded

Cooking down chopped apples helps remove the excess moisture that would otherwise seep out if you were to stir uncooked apples into the batter, which would create dense and mushy muffins. We don’t want those!

If you prefer the texture of shredded apples throughout the muffins, I would recommend shredding on the large holes of a box grater and then cooking as directed in the recipe below, but you will not need to cook the shredded apples as long as the chopped apples.

P.S. I use my favorite swivel peeler to peel apples!

Apple muffin batter mixed together in a glass bowl.

Mix-in ideas

If you want to change up the recipe a bit to suit your tastes or just want to try something different, here are a few ideas:

  • Chopped Nuts: Walnuts or pecans would be delicious! Use ½ to 1 cup in the recipe.
  • Raisins or other dried fruit: Chopped dates or cranberries would be delicious! Add ½ to 1 cup in the recipe.

Topping ideas

If you’d like to skip the cinnamon-sugar topping and try something different, here are a few ideas:

  • Crumble topping: Use the topping from my New York crumb cake and sprinkle over the top of these muffins for something extra special!
  • Chopped Nuts: Toss in a couple of tablespoons of finely chopped walnuts with the cinnamon and sugars for extra crunch.
  • Drizzle with glaze: You can use this in addition to the cinnamon-sugar topping, or on its own. Whisk together 1 cup powdered sugar + 1 tablespoon milk + 1 teaspoon vanilla and drizzle over cooled muffins. You can replace the milk with apple cider or apple juice.

Apple muffin batter in muffin pan.

Muffin pans and liners

Any standard 12-cup muffin pan will work for these muffins. I’ve had the Wilton Everglide Avanti muffin pan for ages, but it is not readily available in most places anymore. If you can’t get your hands on one, my next recommendation is the USA Muffin Pan.

You can spray the pan with non-stick cooking spray or use liners. I’ve used tons of different types of liners over the years, and I absolutely prefer the basic white paper liners. You can find them at just about any grocery store or craft store, but they are incredibly inexpensive if you buy them in bulk online (and they last forever!).

Apple muffin batter topped with cinnamon-sugar before baking.

Storing and freezing instructions

There are a few different options for storing these muffins:

  • Room Temperature – Store in an airtight container at room temperature for up to 3 days.
  • Refrigerator – Kept in an airtight container in the refrigerator, these muffins will stay fresh for up to 1 week.
  • Freezer – Once completely cooled, wrap each muffin in plastic wrap and place in an airtight container or ziplock freezer bag for up to 3 months. Thaw at room temperature.
  • To Reheat – Reheat in the oven (or toaster oven) at 350 degrees F, wrapped in foil, for 15 to 25 minutes. Reheat in a microwave – place on a plate, cover with a damp paper towel and heat for 15 to 30 seconds. In both cases, use the longer time if the muffins were cold or frozen; shorter time if they were at room temperature.

Baked apple muffins still in pan.

More of my favorite muffins:

A basket of apple muffins with one split in half.

If you make the apple muffins and love them, I would so appreciate it if you would take a moment to leave a rating below. Thank you so much! ❤️️

Apple Muffins with Cinnamon-Sugar Topping

These apple-cinnamon muffins pack huge apple flavor thanks to apple cider and chopped apples, with a fabulous cinnamon-sugar crunch on top.
4.73 (33 ratings)


For the Cooked Apples

  • 2 tablespoons (28 g) unsalted butter
  • 2 Granny Smith apples, 6½ ounces each, peeled, cored, and cut into ¼-inch pieces (3 cups)
  • 2 tablespoons light brown sugar
  • ¼ teaspoon (0.25 teaspoon) ground cinnamon

For the Muffins

  • 4 tablespoons (57 g) unsalted butter, melted
  • ½ teaspoon (0.75 teaspoon) ground cinnamon, divided
  • cups (300 g) all-purpose flour
  • teaspoons (2.5 teaspoons) baking powder
  • ¼ teaspoon (0.25 teaspoon) baking soda
  • teaspoons (1.25 teaspoons) salt
  • 1 cup (198 g) granulated sugar
  • 2 eggs
  • ¼ cup (50 g) vegetable oil
  • ½ cup (120 ml) apple cider
  • ½ cup (113 g) plain whole milk yogurt
  • 1 teaspoon vanilla extract

For the Topping

  • 2 tablespoons granulated sugar
  • 2 tablespoons light brown sugar
  • ¼ teaspoon (0.25 teaspoon) ground cinnamon


  • Cook the Apples: Melt the butter in a 12-inch skillet over medium-high heat. Add the apples, brown sugar, and cinnamon. Cook, stirring often, until the moisture has completely evaporated and the apples are well browned, 8 to 10 minutes. Remove the pan from the heat and allow to cool for 10 minutes.
  • Prepare the Muffins: Adjust an oven rack to the upper-middle position and preheat the oven to 400 degrees F. Line a 12-cup muffin tin with paper liners or spray with non-stick cooking spray.
  • In a large bowl, whisk together the flour, baking powder, baking soda, salt and ground cinnamon.
  • In a medium bowl, whisk together the granulated sugar, eggs, oil, and melted butter until thick, about 30 seconds. Whisk the apple cider, yogurt and vanilla into the sugar mixture until combined.
  • Fold the sugar mixture and the cooled apples into the flour mixture until just combined. Divide the batter evenly among the prepared muffin cups (there should be about ⅓ cup of batter per cup, and the cups will be filled to the rim).
  • Mix Together the Topping: In a small bowl, stir together the sugar, brown sugar and cinnamon for the topping. Sprinkle the muffin tops evenly with the topping.
  • Bake: Bake until golden brown and a toothpick inserted in the center comes out with a few moist crumbs attached, 18 to 22 minutes, rotating the muffin tin halfway through baking. Let the muffins cool in the muffin tin on a wire rack for 10 minutes. Remove the muffins from the pan and place on a wire cooling rack. Cool for 5 more minutes before serving. The muffins can be served warm or at room temperature. Store the muffins in an airtight container at room temperature for up to 3 days.


  • Apple Cider: Substitute equal amount of apple juice or other fruit juice (white grape juice is a great neutral-flavored option).
  • Yogurt: Substitute an equal amount of sour cream or whole buttermilk. If using low-fat buttermilk, then only use ¼ cup + 2 tablespoons
  • Add-ins & toppings: See suggested substitutions, combinations, and instructions in the post above.
  • Equipment recommendations: My muffin pan / Another muffin pan / Paper liners / Box grater / Swivel peeler
  • Mini muffins: This recipe will yield 24 mini muffins; bake for 10 to 14 minutes.
  • Quick bread: You can use this batter to bake a quick bread. Spread it in a 9x5-inch loaf pan and bake for 55 to 60 minutes.
  • Storage: Store the muffins in an airtight container at room temperature for up to 3 days or in the refrigerator for up to 1 week.
  • Freezing: Once completely cool, the muffins can be wrapped in plastic wrap and transferred to an airtight container or zip-top bag and frozen for up to 3 months. Thaw at room temperature.
  • Reheat - Reheat in the oven (or toaster oven) at 350 degrees F, wrapped in foil, for 15 to 25 minutes. Reheat in a microwave - place on a plate, cover with a damp paper towel, and heat for 15 to 30 seconds.
  • Recipe from Cook's Country
Nutritional values are based on one serving
Calories: 311kcal, Carbohydrates: 49g, Protein: 4g, Fat: 11g, Saturated Fat: 7g, Cholesterol: 43mg, Sodium: 284mg, Potassium: 180mg, Fiber: 1g, Sugar: 27g, Vitamin A: 240IU, Vitamin C: 1.5mg, Calcium: 67mg, Iron: 1.5mg

Did you make this recipe?

Leave a review below, then snap a picture and tag @thebrowneyedbaker on Instagram so I can see it!

[Photography by Ari of Well Seasoned]