Apple Cinnamon Muffins

A taste of Fall... Gluten-free Apple Cinnamon Muffins with Cinnamon Sugar Crumble topping. Soft & fluffy, packed with apples and so yummy! Bonus: your house will smell amazing while they bake!

gluten free apple cinnamon muffins #glutenfree #glutenfreerecipes
Apple Cinnamon Muffins

Easy, Wholesome and Delicious!

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New! I’ve added a cooking video to this page so you can see how easy it is to make these Gluten-Free Apple Cinnamon Muffins.

If you’re new to this website, there is a printable recipe with exact measurements and directions at the bottom of the page.

Hope you love them!

gluten free apple cinnamon muffins #glutenfree #glutenfreerecipes

Original post:

These Gluten-Free Apple Cinnamon Muffins are one of our favorite muffins, especially in the Fall!

They have the best soft & fluffy texture, are bursting with juicy apples and the most delicious cinnamon sugar crumble!

These muffins were conceived because you all loved our Blueberry Muffins so much and asked if they could be made with apples…

It seemed like a great idea, so we made a few tweaks and created the yummiest Apple Cinnamon Muffins with the same great texture!

Definitely a new Fall favorite, these muffins are moist, light, packed with apples and topped with the yummiest cinnamon sugar crumble!

gluten free apple cinnamon muffins #glutenfree #glutenfreerecipes

And they have such perfect soft and fluffy texture!

They are made with real, whole food ingredients– pantry staples you probably already have in your kitchen– and are adaptable to tastes or dietary needs and they come together quickly.

All you need is:

gluten free flour (we used GF Jules)

baking powder



sugar (or coconut sugar)


butter (or dairy free butter or ghee)

vanilla extract

plain yogurt (or almond milk yogurt)

2 apples

As for the apples, I like to bake with tart apples so these are Granny Smith.  They pair nicely with the crumble topping so that the muffin isn’t too sweet. But any apple you have or love will work!

gluten free apple cinnamon muffins #glutenfree #glutenfreerecipes

And these are very customizable to dietary needs/ preferences.

They can be made them with dairy-free butter sticks, ghee and regular butter.  You can use cane sugar and coconut sugar.  And I’ve made them with milk based and almond milk yogurt.  Each time the recipe works.

As an aside, you may have noticed that we are affiliate for GFJules.  To learn more about why we love GFJules flour and why we have used it for 10 years, click here.

Bonus: at the bottom of that post is a one-time use affiliate Discount Code.

And importantly, purchasing through an affiliate link does not change your cost at all. It generates a small percentage of the sale for me, and purchasing through an affiliate link helps me fund this website and all the recipes I share, so thank you!

Back to the gluten-free Apple Cinnamon Muffins…

The cinnamon sugar crumble is made with sugar, cinnamon and chopped walnuts which adds a nice surprise of texture and flavor but could be easily omitted if you have a nut allergy.

gluten free apple cinnamon muffins #glutenfreerecipes

No matter your preference, give them a try.  They are so yummy!

And so easy to make.

All you do is:

  • mix together the dry ingredients
  • mix the together the wet ingredients
  • then mix the two together.
  • Add in the apples and you’re almost there!

The batter comes together in about 15 minutes but one important tip for best texture and flavor– Be sure to rest the batter for 20-25 minutes prior to filling muffin tins and baking. Don’t rest for more than 30 minutes or the muffins will be too dense.

After the batter has rested, use an ice cream scoop to scoop the batter into muffin tins.

gluten free apple cinnamon muffins #glutenfree #glutenfreerecipes

The sprinkle with the crumble topping and bake!

gluten free apple cinnamon muffins #glutenfree #glutenfreerecipes

Your house will smell amazing while they bake!

And they have the best texture and flavor, and are packed with apples!

gluten free apple cinnamon muffins #glutenfree #glutenfreerecipes

Hope you love them as much as we do!

For more Apple Recipes, have you tried our:

Apple Crumble Bars

Apple Crisp

Apple Coffee Cake

For more muffins and quick breads, click here.

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Scroll down to see the recipe and leave a rating/ comment if you make them. We love hearing from you!



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4.55 from 42 votes

Apple Cinnamon Muffins

Moist, light, packed with apples, and topped with cinnamon sugar crumble, these muffins are a Fall favorite! They stay fresh for several days and freeze well. NOTE: prep time includes letting batter rest for 25 minutes -- only 15 minutes active time.
Prep Time40 minutes
Cook Time25 minutes
Total Time1 hour 5 minutes
Course: Fall, Baking, Breakfast, Snack
Cuisine: Gluten-Free, Dairy-Free Optional
Keyword: easy gluten-free muffins, gluten-free apple cinnamon mufins, reliable gluten-free muffins recipe
Servings: 12 muffins
Author: Healthy Gluten-free Family


  • 2 cups all purpose gluten-free flour containing xanthum gum we used GF Jules
  • 1 tablespoon gluten free baking powder
  • 1/2 teaspoon salt
  • 1 teaspoon cinnamon
  • 3/4 cup cane sugar or coconut sugar
  • 8 tablespoon butter or dairy-free butter or ghee, melted and cooled
  • 1/2 cup plain yogurt or plain almond milk yogurt (we've used low fat, whole milk and greek -- the greek and whole milk yield a moister muffin)
  • 3 large eggs
  • 1 teaspoon vanilla extract
  • 1 1/2 - 2 cups apples skin removed, cup into small cubes, about 1/2 inch NOTE: I always use 2 cups of apples and there is apple in every bite. But if you want more "muffin" and slightly less apples, cut quantity back to 1 1/2 cups.

Cinnamon Sugar Topping

  • 1/4 cup sugar
  • 1 teaspoon cinnamon
  • 1/3 cup finely chopped walnuts Omit if allergic to walnuts


  • In a large bowl, whisk together flour, baking powder, salt, and cinnamon.
  • In a separate bowl, whisk together sugar, melted butter, yogurt, eggs and vanilla until well combined.
  • Mix flour mixture into wet mixture until thoroughly combined and no lumps remain, about 1 minute.
  • Gently fold in apples until evenly distributed.
  • Cover the bowl with plastic wrap and let batter rest at room temperature for 20-25 minutes.
  • Meanwhile, preheat oven to 375 degrees and spray a 12 cup muffin tin with canola oil spray or line with paper muffin cups.
  • While batter rests, combine Cinnamon Sugar Topping ingredients in a small bowl and set aside.
  • Using an ice cream scoop or large spoon, portion batter evenly into prepared muffin tins.
  • Top muffins with cinnamon sugar topping.
  • Bake 25 minutes*, or until the muffins are golden and toothpick inserted in the center comes out clean. *TIP: Check at 20 minutes. If you feel that the tops are browning but want a few more minutes baking the center, gently cover with foil and bake another 5-10 minutes
  • Let muffins cool in muffin tin for 10 minutes. Remove from tins and let cool on wire rack at least another 10 minutes.
Tried this recipe?Mention @healthyGFfamily or tag #healthyGFfamily!

49 thoughts on “Apple Cinnamon Muffins

  1. Your instructions, step 10 tip is incomplete. They look delicious and I’m going to try the recipe. Thanks.

    1. Oops! Sometimes mistakes happen! Luckily that step is about cooking tips and wouldn’t have impacted the recipe… THANK YOU so much for pointing it out! Correcting now! And let me know how you like them!

  2. 5 stars
    I’ve made this recipe twice in the last 5 days!! It is a wonderful grab and go breakfast. I bought GF Jules flour for the second batch and the difference is noticeable.

  3. 5 stars
    I made these yesterday and making them again today! First time making apple cinnamon muffins. They turned out great and very delicious!! Thanks for sharing the recipe!

  4. 5 stars
    LOVED these muffins! I felt like I was back in my grandma’s kitchen. They were so moist and flavorful. Thinking of adding some pumpkin puree (for an extra fall kick) next time but not sure if it will work. Wish me luck!

  5. 5 stars
    Yum! As soon as I gave my family the “okay” to eat they were basically gone – easy recipe to follow and so yummy! I used full fat plain Greek yogurt and was really happy with the texture/consistency.

  6. 5 stars
    I love these! Made a few times now. This time I had some apple butter I made last week handy. So I just added it in (a bit more than 1/4 cup) before resting. Muffins are SO good, with or without the apple butter, but it added some nice flavor and moisture!

  7. If I’m using flour that does not contain xanthum gum, how much xanthum gum do I add? These look delicious! Excited to give them a try!

  8. 5 stars
    I’ve made these muffins 3 times and they turned out great every time! We avoid eggs and dairy also so I used flax eggs and chilled full fat coconut milk (shaken) to sub for eggs and yogurt and it worked great!

  9. Would you be apple to make these with applesauce instead of the apples? My daughter doesn’t like the texture of fruit in things, but likes the flavor.


  10. Hello,
    Can you make these in a mini muffin tray? It would be a better snack size for littles. How would the tep/time be adjusted.

  11. 4 stars
    What is the calories per muffin?
    They are amazing. I haven’t had muffins in over 2 years because I can’t eat gluten.

  12. 5 stars
    These muffins are really delicious. We have made them several times in our house and will keep making them – they are one of our favorite muffin recipes!

  13. 5 stars
    Omg! These are incredible! Such a discovery!
    Every time I make them, people don’t even leave the crumbs, I have already shared your recipe more than 10 times!
    Thank you very much.

  14. 5 stars
    These muffins are amazing! I have made these muffins non stop! They hardly taste gf! I definitely recommend this recipe if you love moist and delicious muffins! So good! I added oats in the cinnamon sugar topping instead of walnuts. Thank you for this amazing recipe!

  15. 5 stars
    This is probably the third year I’ve been making this recipe to kickstart fall in our home 🙂 it’s my husbands favorite muffin I make & probably mine too. The apples inside are the perfect surprise! I like to add a sprinkle of sea salt on top of the cinnamon sugar topping! Thank you for this amazing recipe!

    1. While in most my recipes you can simply use regular all purpose flour if you don’t need to be gluten-free, this one was created with gluten-free flour in mind. That said, it should work fine but no need to let the batter rest. Just mix it and bake the muffins. Let me know if you make them.

  16. 5 stars
    These are so so SO delicious. They smelled amazing while baking so I couldn’t resist trying one out of the oven. Reminded me of a warm Apple strudel! The only sub I made was using Earth Balance Buttery Sticks and an almond milk based yogurt to keep dairy free as well. I will be making these again and again and again. Easily my new favorite muffin (and I love muffins!!).

  17. 5 stars
    These muffins were moist and delicious. I didn’t have any yogurt, so I substituted with 1/2 cup apple sauce and 4 tablespoons ground flax and they came out perfectly.

  18. 5 stars
    These are amazing ! I’ve tried them a couple times already, but this time I want to try making the dough and leaving it in the fridge over night. Would that work ? Or would they come out less fluffy ? Love your content, keep rocking on ! 😉

  19. 5 stars
    Made these for the first time today – will NOT be the last time, as they are delicious!!!!! For the yogurt, I used So Delicious Coconut Yogurt Alternative (plain). I baked these for a bake sale but had to try one to ensure quality ;^). Really, really good.

  20. 5 stars
    I just made these and they’re absolutely delicious! I didn’t have walnuts on hand for the cinnamon sugar topping so I used sliced almonds. But I do have 1 question. What’s the purpose of letting the batter sit for 20 minutes?

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