Healthy Snickerdoodle Muffins Made with Applesauce
Healthy Snickerdoodle Muffins are made with applesauce, coconut sugar, whole wheat flour, and Greek yogurt to keep them healthier than most muffin recipes. Enjoy these fluffy and moist muffins for breakfast or a snack. Ready in 30 minutes!

Snickerdoodle anything is one of my all-time favorite flavors, and muffins are by far my favorite thing to bake, so snickerdoodle muffins were a no-brainer to have on the blog! (My Vegan and Gluten-Free Snickerdoodles AKA Bananadoodles are also my most popular recipe on Hello Spoonful, so it’s obvious you all are fans, too!)
To be honest, I’m not quite sure if snickerdoodle is technically a “flavor” or not, but I’m going with it.
Cinnamon sugar screams fall to me. But cinnamon sugar and apple? Now THAT is the ultimate fall flavor.

These Snickerdoodle Muffins are made healthier by using applesauce and greek yogurt to keep them super moist. I also used half whole wheat flour and half all-purpose to sneak in a little extra fiber.

If you’ve followed me for long, you know how fiber-obsessed I am! There’s a whole chapter about it in my E-Book, not to mention how many times it’s brought up in several of the other chapters.
Normally my baked goods are choc-full of chocolate chips, peanut butter, and all the mix-ins (see: Sweet Potato Chocolate Chip Muffins, Vegan Apple Cinnamon Blondies, Banana Bread Baked Donuts); however, these muffins are one of my favorites and refreshingly simple.
I chose not to add anything into the batter because the flavor is truly delicious and I didn’t want anything crowding the cinnamon sugar taste.
BUT, feel free to add in apple chunks, chocolate chips, or nuts as you please!
I also prefer mine warmed up with a tall glass of vanilla almond milk. 🙂

Healthy Snickerdoodle Muffins Ingredients
- Flour – I am using white whole wheat flour but all purpose will also work!
- Sugar – I am using a blend of Coconut Sugar and Brown Sugar
- Ground Cinnamon – You can’t have snickerdoodles without cinnamon!
- Eggs
- Unsweetened Applesauce – this allows us to keep the snickerdoodle muffins low in added sugar and oils
- Greek Yogurt – Greek yogurt adds moisture and protein!
- Unsalted Butter
- Other baking essentials: Baking Powder, Baking Soda, vanilla extract, Salt

How To Make Healthy Snickerdoodle Muffins:
- Preheat the oven to 375F degrees. Line a muffin pan with muffin papers.
- Sift together the flour, cinnamon, baking powder, baking soda, and salt.
- In a large bowl whisk together the melted butter and sugars. Then whisk in the eggs, vanilla extract and applesauce.
- Whisk about 1/2 of the flour mixture into the wet ingredients, then gently fold in the rest using a rubber spatula or wooden spoon.
- Spoon the batter into the prepared muffin pan.
- Bake for 17-22 minutes, or until the tops are slightly firm to the touch and an inserted toothpick comes out clean. Cool for 10 minutes.
- Dip the top of a warm muffin in the melted butter, shaking off any excess. Then dip the top in the bowl of cinnamon sugar. Repeat the process with the rest of the muffins. OR wait until the second day and roll the muffins into the cinnamon sugar without any butter. The tops will get moist and won’t need any butter to help it stick.
These Snickerdoodle Muffins are quickly becoming one of my favorite recipes of all-time! Even my not-so-healthy friends have been loving them, too.
Love snickerdoodles? Be sure to try one of my other snickerdoodle recipes!
- Almond Flour Snickerdoodles
- Gluten-Free Snickerdoodle Cookie Dough Balls
- Bananadoodles: Gluten Free + Vegan Snickerdoodles
- Soft Baked Pumpkin Snickerdoodle Cookies with White Chocolate Chips
- Snickerdoodle Vegan Blended Baked Oats
I can’t wait to hear what you all think! Don’t forget to tag me on Instagram when you make them!
PIN ME FOR LATER

Healthy Snickerdoodle Muffins with Applesauce
Ingredients
Muffins
- 2 Cups White whole wheat flour
- 1/2 Cup Coconut Sugar
- 1/4 Cup Brown Sugar
- 2 Tsp Ground Cinnamon
- 1 1/2 Tsp Baking Powder
- 1/2 Tsp Baking Soda
- 1/2 Tsp Salt
- 2 eggs
- 1 Cup Unsweetened Applesauce
- 1/4 Cup Unsalted Butter melted
- 2 tbsp Greek Yogurt I used 2%
- 1.5 Tsp Pure Vanilla Extract
Topping
- 1/4 Cup Brown Sugar
- 1 Tsp Cinnamon
- 1/3 Cup Butter Melted
Instructions
Muffins
- Preheat the oven to 375F degrees. Line a muffin pan with muffin papers.
- Sift together the flour, cinnamon, baking powder, baking soda and salt.
- In a large bowl whisk together the melted butter and sugars. Then whisk in the eggs, vanilla extract, greek yogurt, and applesauce.
- Whisk about 1/2 of the flour mixture into the wet ingredients, then gently fold in the rest using a rubber spatula or wooden spoon.
- Spoon the batter into the prepared muffin pan.
- Bake for 17-22 minutes, or until the tops are slightly firm to the touch and an inserted toothpick comes out clean. Cool for 10 minutes.
Topping
- In a small bowl whisk together the brown sugar and cinnamon.
- Dip the top of a warm muffin in the melted butter, shaking off any excess. Then dip the top in the bowl of cinnamon sugar. Repeat the process with the rest of the muffins OR wait until the second day and roll the muffins into the cinnamon sugar without any butter. The tops will get moist and won’t need any butter to help it stick.
I used soft white winter wheat for the fresh milled cup of flour and added cinnamon chips… I didn’t want to do the whole dip in butter step at the end, so I just sprinkled cinnamon sugar on top before baking. Definitely a rare treat for us, but WOW! Delicious!!!
Thanks so much for the kind review and rating! I truly appreciate it and am so glad you enjoyed the recipe! 🙂
When do you add the Greek yogurt?
With the other wet ingredients 🙂
These look AMAZING! Would it be possible to give me the nutritional info? Also, can an egg substitute be used as well as Swerve instead of coconut sugar?
Thank you! I have only made the recipe as listed so I can’t say for sure, but I’m sure you can google how to swap them and what ratio to use 🙂 I don’t provide nutritional information but you can input it into a calculator online!
Loved these! I rolled them in sugar each morning before carrying them to work.
That sounds SO good!! Glad you’re enjoying them!
Wow, they look so delicious!!