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!

Sky-High Apple Pie Muffins

Yield: 14-16 muffins

Print Recipe



  • 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 packed 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. Cover leftover muffins tightly and store at room temperature for up to 5 days. Muffins may be frozen, up to 2-3 months.

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?


172 Responses to “Sky High Apple Pie Muffins.”

  1. #
    Danielle Myrandposted November 11, 2014 at 7:20 pm

    Please, can you tell me how much calories in double chocolate muffins. ??

    They are awesome. Thiank you.


  2. #
    Sueposted February 9, 2015 at 9:06 am

    These were fantastic-have made them twice now- I used 2Tbsp. canola oil and 2Tbsp. applesauce These were a hit with the kids!


  3. #
    Clare-marieposted February 26, 2015 at 9:38 pm

    Hi there, I made these lovely muffins with 3 cups rye flour & 1/2 cup rolled oats. ( we cant eat wheat ) they were wonderful! Thankyou. Xx


  4. #
    Kristaposted March 6, 2015 at 12:56 pm

    Hi Sally,

    I made these muffins yesterday, and they are INCREDIBLE! They have all the taste of a regular muffin but only 1/3 of the calories! I am thinking next time I might try a blueberry/lemon combo.

    I noticed that you live in Philly and that you are a runner. Are you running the Hot Chocolate 15K in Philly on April 4th? You get a chocolate bar medal…how perfect is that? Obviously, it’s not edible, but it’s pretty cool! It should be a fun race.



  5. #
    Kristaposted March 6, 2015 at 1:35 pm

    Hi Sally,

    I made these muffins yesterday, and they are INCREDIBLE! They have all the taste of a regular muffin but only 1/3 of the calories! I am thinking next time I might try a blueberry/lemon combo.

    I noticed that you live in Philly and that you are a runner. Are you running the Hot Chocolate 15K in Philly on April 4th? You get a chocolate bar medal…how perfect is that? Obviously, it’s not edible, but it’s pretty cool!



    • Sallyreplied on March 7th, 2015 at 8:18 am

      Hey Krista! I did not know about this race! I’ll look it up. I won’t be able to run it this year, but maybe next year. A chocolate bar medal… how can any runner resist?


  6. #
    Vanessaposted March 13, 2015 at 9:02 pm

    Hi Sally! I love this recipe and was wondering if it would work well as a bread?


    • Sallyreplied on March 14th, 2015 at 2:37 pm

      I’m unsure it would! I do not know the bake time.


  7. #
    Tamie Shawposted March 25, 2015 at 11:30 am

    Hi Sally, I was wondering approximately how many calories are in the apple muffins. You might of posted it but I didn’t happen to see.
    Made them last night and they went over Great with my family.
    My Mom loves her sweets so I was worried they wouldn’t be sweet enough for her but she Loved them!
    thanks Tamie


    • Sallyreplied on March 25th, 2015 at 3:46 pm

      I’m unsure of the calories in most of my recipes– sorry!


  8. #
    Rhondaposted April 4, 2015 at 12:34 pm

    loved your tip to crank the heat to 425 the first 5 minutes and then finish these D-Lish muffins at 375. My family is loving the sky high muffins for breakfast right now – warm and fresh out of the oven.


  9. #
    Kaitposted July 18, 2015 at 11:11 am

    Thank you for such a kick ass recipe! I subbed applesauce for more yogurt, which seemed to work fine. Hearty, tasty, not-too-sweet apple muffins. I totally needed a little taste of fall in July. 


  10. #
    Staceyposted September 4, 2015 at 2:50 pm

    These turned out better than expected. Kids loved them and looked like something out of a bakery. I made these with a few adjustments since I ran out of yogurt. I used the applesauce and oil in place of the yogurt and used buttermilk for milk. Delicious. I will be making lots more since iI have an abundance of apples on our trees this year.


  11. #
    Daleposted September 12, 2015 at 7:43 am

    These are wonderful.. made them with regular white flour and oil…. having one right now with my coffee…popped in the microwave 20 seconds…. I’m in heaven… love your muffins:)))


  12. #
    Rosaposted September 24, 2015 at 12:59 pm

    Hi Sally recipe looks fab – looking for something to do with my cooking apples do you think this will work in these? 


    • Sallyreplied on September 24th, 2015 at 7:09 pm

      Yes, definitely.


  13. #
    Jenposted October 11, 2015 at 9:45 am

    Hi Sally – I was looking for a healthy apple muffin recipe and these look great. I’m wondering about the apple sauce, though. I have a lot of apples here, and no apple sauce, so I thought I’d make it myself. But are you using sweetened or unsweetened applesauce in the recipe. I’ve been trying to use as little sugar as possible when baking, but I don’t want them to be tasteless either. Thanks!


  14. #
    Carolineposted October 18, 2015 at 12:53 pm

    These were absolutely divine!!! Thank you so much!


  15. #
    Cassie Millerposted October 28, 2015 at 9:57 pm

    Wow! I just made these tonight, and they turned iut great! I’ve never actually made a muffin that was not flat so this was really fun and they looked perfect. I will definitely use this recipe as a base for more muffins in the future, thanks!


  16. #
    Jordanposted December 5, 2015 at 5:05 pm

    Sally can I use sour cream instead of yoghurt in your muffin recipes 


  17. #
    Laylaposted July 10, 2016 at 9:18 pm

    Hi Sally,

    I’m not sure what I did wrong but these came out very gummy in the middle. I used frozen blueberries and coconut sugar instead of brown sugar. Any idea why they would have come out that way? I’ve used many of your other recipes and they usually come out perfect!


  18. #
    Alexandraposted September 23, 2016 at 2:34 pm

    Hi Sally! First I want to tell you how much I love your site, your recipes and everything you post and also I want to thank you for sharing that. I have a question for you, how can I replace yogurt in your muffin recipes? I have a cousin visiting in my house these days but her daughter is lactose and gluten allergic, I can use gluten free baking  flour and soy milk but what can I do about the yogurt? I’d really appreciate if you can help me, thanks a lot


    • Sallyreplied on September 25th, 2016 at 9:31 am

      Who about a dairy free yogurt? That should work!


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