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two photos of apple pie muffins

I am quite certain that there is nothing in this world comparable to a warm, freshly baked muffin to wake up to in the morning.

Typically, most muffins you find in bakeries are cupcakes in disguise – relying heavily on oil, butter, and cups of sugar for their sweetness. When I’m craving a healthier muffin, I like to make them at home. These applesauce muffins and healthy apple muffins are two other favorites I often turn to.

These homemade apple pie muffins are soft, fluffy, and full of good-for-you ingredients like whole oats and fresh apples. In lieu of butter and oil, I use yogurt and applesauce to give the muffins some moisture.

apple pie muffins
sky high apple pie muffins

What I love most about these muffins is that they are SKY HIGH. It’s taken some practice, but I finally found a few tricks to bake up mile high, fluffy muffins – no more flat muffins here. How to bake high-domed, fluffy muffins:

  • You need a very, very thick batter. Much thicker than cake or cupcake batter – you want “spoonable” batter, not “pourable.”
  • Do not over-mix the batter- this will create tough + flat muffins.
  • Fill muffin pan cups all the way to the top, even a bit higher. Filling only 1/2 or 2/3 of the way to the top is not enough batter to produce a high-domed muffin.
  • Start off with a very oven hot temperature, then lower it down – doing this lifts the muffin top up quickly and creates a tall crust. Typically, muffins are baked at 350F – 375F the whole time, but set the oven to 425F initially, then bring back down to 350F or 375F.

I also love these apple muffins with blackberries and apples. Replace 1 cup of the apples with 1 cup of fresh or frozen blackberries. In the pictured apple blackberry muffins below, I skipped the oat streusel made with butter and simply mixed 3 Tablespoons of oats + 1 Tablespoon brown sugar. Sprinkle that over each muffin before baking.

blackberry apple muffins on a white plate

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overhead photo of apple pie muffins

Sky-High Apple Pie Muffins

  • Author: Sally
  • Prep Time: 15 minutes
  • Cook Time: 20 minutes
  • Total Time: 50 minutes
  • Yield: 1416 muffins 1x
  • Category: Muffins
  • Method: Baking
  • Cuisine: American


Homemade sky high apple pie muffins are soft, fluffy, and full of good-for-you ingredients like whole oats, fresh apples, and white whole wheat flour!



Oat Streusel Topping

  • 1/4 cup packed dark brown sugar
  • 2 Tablespoons all-purpose flour (spoon & leveled)
  • 2 Tablespoons old-fashioned rolled oats
  • 1/2 teaspoon ground cinnamon
  • 2 Tablespoons unsalted butter, melted


  • 3 cups white whole wheat flour or all-purpose flour (spoon & leveled)
  • 2 teaspoons baking powder
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon salt
  • 1 and 1/2 teaspoons ground cinnamon
  • 1/2 teaspoon ground nutmeg
  • 1 cup unsweetened almond milk (or any dairy or nondairy milk)
  • 1/2 cup packed light or dark brown sugar
  • 1/4 cup granulated sugar
  • 1/3 cup plain or apple-flavored yogurt
  • 1/3 cup unsweetened applesauce*
  • 2 large eggs
  • 2 heaping cups chopped apple (peeled or not peeled—your choice)


  1. Preheat oven to 425°F (218°C). Spray muffin tin with nonstick spray. Set aside.
  2. Prepare oat streusel topping by mixing everything together until the mixture resembles coarse crumbs. Set aside.
  3. Prepare the muffins: In a large bowl whisk the flour, baking powder, baking soda, salt, cinnamon and nutmeg. Set aside. In a separate large bowl, whisk together the milk, sugars, yogurt, applesauce, and eggs. Whisk wet ingredients into the flour mixture, mixing until *just combined* – do not over-mix. Gently fold in the apples.
  4. Spoon the batter into 12 lined muffin cups, making sure each one is filled to the very top. Lightly press a heaping spoonful of oat streusel into the tops of each muffin.
  5. Bake for 5 minutes at 425°F (218°C), then immediately reduce the oven temperature to 375°F (191°C) and bake for another 15-18 minutes, or until a toothpick inserted in the center comes out clean. Cover leftover muffins tightly and store at room temperature for up to 5 days.


  1. Freezing Instructions: Muffins may be frozen, up to 2-3 months.
  2. Applesauce: The unsweetened applesauce gives these muffins moisture- just as oil would – without the added fat. Feel free to use vegetable oil instead of applesauce.
  3. Yogurt: In my muffins, I used Chobani 0% Apple Cinnamon flavor. If you can’t find an apple flavored yogurt, plain or vanilla yogurt would work as well.

Keywords: apple pie muffins

Reader Questions and Reviews

  1. Hi Sally,

    Will quick cooking oats do instead of old fashioned oats?

    Thanks 🙂

  2. Hi sally!! Love your recipes!! I don’t have any kind of yogurt.. What else could i possibly use?..

    1. Hi Lydia! (Additional) unsweetened applesauce or sour cream make wonderful substitutions for the yogurt.

  3. Followed this recipe exactly with plain chobani Greek yogurt. These are delicious. They don’t taste “healthy” except for the fact you feel full after eating one, which makes them a nice option for breakfast. I love them. Also house smells amazing. Thanks for recipe!

    1. I’m unsure of the nutritional info of this recipe, but there are many great online calculators like this one:

  4. I usually never even think about adjusting any of Sally’s recipes, but this time I needed a gluten free muffin. I substituted a gluten free all purpose flour in these and the muffins turned out fantastic!!!

  5. Made these muffins on a snowy and cold morning up in Canada. They are delicious! Thank you for ALL the great recipes.

  6. Absolutely in love with your blog! I was actually wondering if we would be able to sub half of the oil for applesauce for this recipe? (or most of your muffin recipes; they all sound phenomenal!) Thanks a ton 🙂

    1. Hi Faren, There is no oil in this recipe – only applesauce and yogurt!

  7. I was wondering if I could make this into mini muffins, because I don’t have a normal sized muffin tin. Is there a conversion for mini ones? Thank you!

    1. Sure can! For mini muffins, the bake time will be around 8-10 minutes at 375. No need for a higher temp with such small muffins.

      1. You can, but you don’t have to – you will just have more mini muffins 🙂

  8. A regular in your amazing baking group just made these so I came to get the recipe. I only have semi jumbo muffin tins for now (not the wide ‘big box store’ style, I have Wilton tins). Have you any idea how to adjust bake time & temp for these made in the larger tins? Thanks!

    1. Hi Elizabeth, If we have tested a different size pan it will be listed in the recipe notes. For any shapes/sizes that are not listed, you can use our handy Cake Pan Sizes & Conversions post to help calculate how much batter you would need for different size pans.

  9. Absolutely delicious! Especially enjoyed the sweet apples with the tart blueberries and the crunchy streusel on top.

  10. Just like the name itself, SKY HIGH APPLE PIE and you will definitely have the sky high muffins. It’s a very interesting recipe, quite surprised with how thick the batter is. But don’t worry, you’ve done nothing wrong (as long as you follow the recipe closely). It’s definitely great muffins, very fluffy, aromatic, and fulfilling. Perfect muffin for breakfast with your favourite coffee uhh yeaahhh *closing my eyes* My heart beats for this recipe, feels like falling in love (butterflies in my stomach).

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