Sky High Apple Pie Muffins

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 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: 14-16 muffins
  • 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!



  • 3 cups white whole wheat flour or all-purpose flour (spoon & leveled)
  • 1 and 1/2 teaspoons ground cinnamon
  • 1/2 teaspoon ground nutmeg
  • 1 cup almond milk (or soy or regular)
  • 1/2 cup packed dark brown sugar
  • 1/4 cup + 2 Tablespoons fat free apple yogurt*
  • 1/4 cup unsweetened applesauce*
  • 1/4 cup granulated sugar
  • 2 large eggs
  • 3 and 1/2 teaspoons baking powder
  • 1/2 teaspoon salt
  • 1/8 teaspoon baking soda
  • 2 heaping cups chopped apple (cored + peeled, if you prefer peeled chunks – I did not peel mine)

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


  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 course crumbs. Set aside.
  3. Prepare the muffins: in a large bowl combine the flour, cinnamon and nutmeg. Set aside. In a separate large bowl, whisk together the milk, sugars, yogurt, apple sauce, eggs, baking powder, salt and baking soda. Gently fold wet mixture into the flour, stirring until *just combined* – do NOT overmix. Gently fold in the apples.
  4. Spoon the batter into 12 muffin tins, making sure each one is filled to the very top. Sprinkle reserved oat streusel topping over each muffin.
    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 in lieu of the applesauce, which would lend a softer muffin with a higher fat content.
  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

My Strawberry Banana Muffins are completely fat free and weigh in at only 90 calories each. They are FULL of flavor thanks to the mashed banana and applesauce. Applesauce is my secret weapon in baking- use it to replace oil or butter. And you can’t even taste the apple!

Single Serving Chocolate Chip Muffin is perfect when I don’t have time or a need to bake an entire batch of muffins. It is low fat, whole wheat, and full of chocolate chunks. Sometimes I just don’t need 11 extra muffins laying around!

1 single serving chocolate chip muffin

 Nutella Stuffed Cinnamon Sugar Muffins aren’t quite as healthy as today’s muffins, but they sure are tasty anytime of day. Plus, how can one resist that crunchy cinnamon sugar coating?

cinnamon sugar Nutella muffins on a yellow and white plate with a bite taken from a muffin showing the Nutella filling


  1. Hi Sally,

    Will quick cooking oats do instead of old fashioned oats?

    Thanks 🙂

  2. Bethanie Hughes says:

    Could I make these using granny smith apples? I have a ton to use up

    1. Definitely.

  3. 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.

  4. Betsy Hendley says:

    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!

  5. Judy Christenson says:

    I was hoping to find nutrition information to go with your recipes?

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

  6. 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!!!

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

  8. 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!

  9. 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. Stephanie @ Sally's Baking Addiction says:

      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. Thank you! Would I have to half the recipe?

      2. Stephanie @ Sally's Baking Addiction says:

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

  10. 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. Michelle @ Sally's Baking Addiction says:

      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.

  11. My family really loved these muffins!

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I’m Sally, a cookbook author, photographer, and blogger. My goal is to give you the confidence and knowledge to cook and bake from scratch while providing quality recipes and plenty of pictures. Grab a cookie, take a seat, and have fun exploring! more about Sally