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

  • 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
  • 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!

 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?


  1. I really wanted these to work out as beautifully as in the photo. Mine did turn out to be sky high, but I still found them to be quite dense and bland. I make skinny and vegan muffins often, so I’m used to baking with applesauce and low oil, but I’ve never had something turn out as heavy as these. They looked pretty, but I didn’t want to eat them. Next time I’ll use oil and more spices.

  2. Hi Sally – I’ve made your sky-high sparkly blueberry muffins several time now and they are always a hit. Can I substitute the almond milk with buttermilk and the applesauce/oil with coconut oil, like in the blueberry recipe? I have an apple orchard behind my house and the pickers generously give us a few bags of apples so I wanted to try the apple muffins. Thanks!

    1. Hi Marilyn. So sorry for the delay responding. I was on vacation. Buttermilk would be just fine and 1/4 cup melted coconut oil would be great as well. Hope you enjoy!

  3. I just put these in the oven but I think i did something wrong. Because I put in the applechunks and the flour together and mixed it, very carefully. The batter was pretty runny I thought but Im hoping it will turn out okay. They arent skyhigh so I think I did something wrong there as well. But that is a learningthing, as long as it tastes good I’m happy. . It smells great already, so fingers crossed!!

  4. I just ate them (well, one of them) and they turned out great. They were indeed skyhigh, so I did nothing wrong and the inside was good as well. Very apply and very yummy. I put some cinnamonsugar on top of the strueseltop, and I loved it. I used Schar glutenfree cakeflour and it turned out great. I am going to try other muffins and cakes from your site with this flour because your recipes look so yummy and I really love to bake (with glutenfree flour that actually works).

  5. Wow—I just made these today and they were amazing! I am a novice at baking and didn’t expect them to be this good. They rose beautifully and really were sky-high! I didn’t have any nutmeg, so I omitted it. It was still great. I hate the fact that most muffin recipes are just cupcakes in disguise. These really are muffins!

  6. I made these muffins this morning and myself, my husband and 3 kiddos were so impressed. My husband, who doesn’t like whole grain and shudders at yogurt didn’t notice that there was anything in these muffins that he didn’t like. I used fat free lemon Greek yogurt (because I didn’t have any plain, vanilla or sour cream) and added a splash of vanilla to the wet ingredients…absolutely fantastic. Thank you so much!

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

  8. 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

  9. 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.


  10. 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!


    1. 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?

  11. 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

  12. 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.

  13. 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. 

  14. 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.

  15. 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:)))

    1. Hola Sally soy de Argentina. Quisiera tener tus manos. Buscaba muffins sin tacc y te encontre. Si tuvieras alguna receta para celiacos por las proporciones basicamente, te lo agradecería mucho! Sos fabulosa!

  16. 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!

  17. 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!

  18. 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!

  19. 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

  20. 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:

  21. 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!!!

1 2 3

Leave a Reply

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.

With kitchen-tested quality recipes and step-by-step tutorials, my goal is to give you the confidence to bake and cook from scratch.

Recipes You’ll Love



Sally's Baking Challenge

Join the community on the 1st of every month as we tackle a new challenge recipe.

View More

Sally's Cookie Palooza

A tradition since 2013, every December we countdown to Christmas with 10 new cookie recipes in a row!

View More

Sally's Pie Week

The first week of every November is all about Thanksgiving Pies.

View More

My Cookbooks

About Sally

Welcome to my Kitchen!

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