Sky High Apple Pie Muffins.

Sky High Apple Pie Muffins. Learn how to make bakery-style (and healthier!) muffins at

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.  Bonus points if it’s healthy!

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 healthy muffin, I find the only way I can truly enjoy them is to just make them myself.  Plus they make my apartment smell like a bakery. ;)

These homemade low fat apple pie muffins are soft, fluffy, and full of good-for-you ingredients like whole oats, fresh apples, and white whole wheat flour.  In lieu of butter and oil, I used fat free yogurt and applesauce to give the muffins their moisture.  I also used as little sugar as possible – but feel free to reduce the amount of sugar or add more, depending on your tastes.

What I love most about these guys is that they are SKY HIGH.  I’m talking super tall bakery sized muffins.  Flat muffins??  No thank you. It’s taken some practice, but I finally found a few tricks to bake up mile high, fluffy muffins – no more flat, dry 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 overmix the batter- this will create hard, tough, + flat muffins.
  • Do not be afraid to fill your muffin tins.  Fill all the way to the top.  Filling your muffin tins only 1/2 or 2/3 of the way to the top is not enough batter to produce a high-domed muffin.  Fill to the brim.
  • Start off with a very oven hot temperature, then lower it down – doing so 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.

You better believe that each muffin I bake from now on will be tall and sky high, just like these.  Enjoy!

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Sky-High Apple Pie Muffins

Yield: 14-16 muffins



  • 3 cups white whole wheat flour (or all-purpose flour)
  • 1 and 1/2 tsp ground cinnamon
  • 1/2 tsp ground nutmeg
  • 1 cup almond milk (or soy or regular)
  • 1/2 cup dark brown sugar, packed
  • 1/4 cup + 2 Tbsp fat free apple yogurt* (or vanilla or plain)
  • 1/4 cup unsweetened apple sauce (or vegetable oil)
  • 1/4 cup sugar
  • 2 large eggs
  • 3 and 1/2 tsp baking powder
  • 1/2 tsp salt
  • 1/8 tsp 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 dark brown sugar
  • 2 Tbsp all-purpose flour
  • 2 Tbsp old-fashioned rolled oats
  • 1/2 tsp ground cinnamon
  • 2 Tbsp unsalted butter


Preheat oven to 425F. Spray muffin tin with nonstick spray. Set aside.

Prepare oat streusel topping by mixing everything together until the mixture resembles course crumbs.  Set  aside.

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.

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 degrees, then immediately reduce the oven temperature to 375 degrees and bake for another 15-18 minutes, or until a toothpick inserted in the center comes out clean.

Sally's Notes: *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. 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.

© Sally’s Baking Addiction. All images & content are copyright protected. Please do not use my images without prior permission. If you want to republish this recipe, please re-write the recipe in your own words, or link back to this post for the recipe.



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!


 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?


122 Responses to “Sky High Apple Pie Muffins.”

  1. #
    Rosieposted April 24, 2014 at 7:50 pm

    These look absolutely DELICIOUS! When I saw the pictures of these I just had to bake some :) But I don’t have any ground nutmeg…is there a substitute for them that you would recommend? I don’t want to substitute the wrong thing! :)


    • Sallyreplied on April 24th, 2014 at 8:45 pm

      I would simply leave it out, Rosie. Enjoy!


  2. #
    Soumyaposted April 24, 2014 at 11:49 pm

    These came out extremely well! I had never made streusel before, so I was a bit skeptical but it was so yummy! I gave the muffins to my neighbors as well and they absolutely loved it!! I have only one ques-my streusel did not stick to my muffins after baking. It was crumbly(in a good way) and some of it fell while picking out the muffins from the muffin stand. Could you tell me what did I do wrong?


    • Sallyreplied on April 25th, 2014 at 7:12 am

      That’s simply because there is no butter in the streusel. It’s supposed to be crumbly – try pressing down on the streusel after topping the muffin batter with it. That will help it adhere.


      • Soumyareplied on April 25th, 2014 at 11:09 am

        Thanks for the tip!

  3. #
    Robinposted May 7, 2014 at 10:53 am

    Hi Sally,

    I have whole wheat flour and AP flour on hand. Would you recommend subbing all AP flour for the white whole wheat flour or could I do a combo of part whole wheat and part AP? If so, in what ratio do you recommend?


    • Sallyreplied on May 7th, 2014 at 1:55 pm

      I recommend all all-purpose flour. Or you can do half AP and half whole wheat.


  4. #
    Elsieposted June 19, 2014 at 3:21 am

    Hello! These muffins sounds great, thank you for sharing this recipe! Just wondering if you would recommend using 1/8 cup applesauce and 1/8 cup canola oil instead of all applesauce or all oil? I like having a little oil for the softness of the muffin but not too much you see!


    • Sallyreplied on June 19th, 2014 at 7:54 am

      Hey Elsie! Yep, 1/8 of each would be just fine. Enjoy!


  5. #
    Alexposted June 19, 2014 at 2:41 pm

    Would you be able to use Greek yogurt instead of a regular yogurt?


    • Sallyreplied on June 20th, 2014 at 9:51 am

      Yes, that would be fine.


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