Vegan Apple Crisp Muffins

Created by Laura Wright
5 from 16 votes

These vegan apple crisp muffins are comforting, sweet, perfectly spiced, tender, and delicious! Spiced chunks of apples are folded into the batter and topped with a buttery oat crumble. A perfect weekend treat with simple ingredients.

An overhead shot of baked vegan apple crisp muffins set upright in a muffin tin with apples in some of the muffin cups.
An overhead shot of crumble topped muffins set inside of a pink linen in a bowl. An apple is shown to the side.
An overhead shot shows diced apples sautéing in a skillet.
An overhead shot of ingredients for vegan apple crips muffins.
Two images show crumble topping as a mixture before being combined and after in a light green bowl.

I was fully in the mood for some apples, buttery oat topping, and spice! Old fashioned apple crisp is in my top 3 desserts of all time. I did go back and forth on calling these vegan apple crisp muffins or apple crumble muffins. Kind of the same thing though, right? Either way, apple crisp muffins sounds cozier to me. We are all about the cozy lately.

I think I’ve talked about this before, but my taste for coconut sugar kind of waned in the last few years. I realized that I was using it repeatedly as a “healthier” alternative to sugar even though I wasn’t crazy about the taste. If I’m having a treat, I’m making it with ingredients that I actually like these days. So I went all brown sugar and vegan butter in these! They really are so delicious, tender, buttery, and sweet.

I make the topping first and let it firm up in the fridge. While that’s happening, I sauté the apples with cinnamon, and then I let them cool a bit. The muffin batter comes together simply enough! I fold some of the apples into the muffins with the remaining pressed into the tops. I purposely made lots of crunchy oat topping in this recipe! We sprinkle that on top and bake until golden brown.

More Vegan Muffin Goodness

I made these cozy muffins with some of my favourite Flourist sifted red spring wheat flour, local apples, and I was also lucky enough to score some of Diaspora Co’s cinnamon release! I suggest lots of alternatives for the flour in the recipe notes (along with a million other things haha). Hope that you get a chance to try one of these with an extra swoop of vegan butter and a cup of tea soon!

A head-on shot of a jar of ground cinnamon, a bottle of apple cider vinegar and a brown paper bag of flour.
A 3/4 angle image shows cooked diced apples being added to muffin batter in a large white bowl.
Image shows muffins topped with a crumble topping pre-baking.
An overhead shot of crumble topped muffins set inside of a pink linen in a bowl. An apple is shown to the side.
Image shows a vegan apple crisp muffin split in half and spread with swoops of vegan butter on both sides.

Extra Cozy Vegan Apple Crisp Muffins

These vegan apple crisp muffins are comforting, sweet, perfectly spiced, tender, and delicious! Spiced chunks of apples are folded into the batter and topped with a buttery oat crumble. A perfect weekend treat with simple ingredients.
5 from 16 votes
An overhead shot of crumble topped muffins set inside of a pink linen in a bowl. An apple is shown to the side.
Prep Time: 15 minutes
Cook Time: 30 minutes
Total Time: 45 minutes
Servings 12



  • ½ cup white whole wheat flour
  • ¼ cup granulated cane sugar
  • ¼ cup brown sugar
  • cup rolled oats
  • ½ teaspoon ground cinnamon
  • teaspoon fine sea salt
  • 5 tablespoons cold vegan butter, chopped into small pieces


  • 1 tablespoon vegan butter
  • 2 cups small diced apples (from approximately 2 small-ish apples)
  • 1 ½ teaspoons ground cinnamon, divided
  • ¾ cup unsweetened non-dairy milk
  • ¾ teaspoon apple cider vinegar
  • 1 ½ teaspoons ground flax seeds
  • 2 cups white whole wheat flour
  • 1 cup brown sugar (not packed)
  • 1 teaspoon baking powder
  • ½ teaspoon baking soda
  • ½ teaspoon fine sea salt
  • teaspoon freshly grated nutmeg
  • 6 tablespoons sunflower oil (or other neutral-tasting oil of choice)
  • 2 tablespoons unsweetened applesauce
  • 2 teaspoons vanilla extract
  • 1 teaspoon finely grated lemon zest


  • Flourist’s sifted red spring wheat flour is my go-to for pretty much everything. For folks that haven’t used it before, I always liken it to white whole wheat flour. If you’re looking to substitute, you could use equal amounts of light/sifted spelt flour, all purpose flour or a 50/50 mix of whole wheat flour and all purpose flour.  
  • I know that some folks have played around with gluten-free flour blends in my muffin recipes before and have had success, but I cannot personally vouch for any one particular blend/brand with this recipe. 
  • If you’ve used recipes from my site before, you likely already know this: Miyoko’s cultured vegan butter is my vegan butter of choice. 
  • If you’re using pre-ground nutmeg, you can increase the amount to ¼ teaspoon. 
  • If you’re partial to coconut palm sugar, you can definitely substitute one-for-one for the brown sugar in the muffin batter. For the topping, my hunch is that the coconut palm sugar would separate from the fat as it bakes. If you’re willing to try it in the topping though, I would start with ⅓ cup of coconut palm sugar to replace BOTH the cane sugar and the brown sugar. See how the mixture is clumping up and feeling (should be like slightly wet sand), and go from there. 
  • I used local Jonagold apples here.


  • Preheat the oven to 400°F. Lightly grease a standard muffin tin, or apply paper/silicone liners to the cups.
  • Make the topping. In a medium bowl, combine the ½ white whole wheat flour, cane sugar, brown sugar, oats, cinnamon, sea salt, and vegan butter. Using a spoon, stir everything together to get the vegan butter pieces coated in the flour mixture. Then, using your hands, start combining the mixture by pressing the pieces of butter between your fingers. Keep going until you have a slightly wet sand-like texture and a uniform, crumbly consistency. Set the topping aside in the fridge.
  • Place a small sauté pan over medium heat. Add the tablespoon of vegan butter to the pan and swirl it around. Add the chopped apples to the pan along with ½ teaspoon of ground cinnamon. Stir to combine. Keep sautéing the apples until they are slightly softened, about 3 minutes. Take the apples off the heat and allow them to cool slightly.
  • In a small bowl, combine the non-dairy milk, apple cider vinegar, and ground flax seeds. Stir to combine and set aside for 5 minutes.
  • In a large bowl, combine white whole wheat flour, brown sugar, baking powder, baking soda, sea salt, nutmeg, and the remaining 1 teaspoon of ground cinnamon. Stir to combine.
  • In the small bowl with the non-dairy milk and flax mixture, whisk in the sunflower oil, applesauce, vanilla, and lemon zest. Once combined, add that mixture to the large bowl with the flour mixture. Add about ⅔ of the sautéed apples to the bowl as well. Using a rubber spatula, stir everything together until JUST combined and there are no large pockets of dry ingredients.
  • Using a ⅓ cup measure, portion out the muffin batter evenly into all of the muffin cups. Top the portions of batter with the remaining sautéed apples. Retrieve the oat topping from the fridge and evenly distribute it amongst the tops of the muffins. This is a fair amount of topping, so you’ll have to push it into the tops of the muffins.
  • Bake the muffins until the tops are golden brown and a paring knife inserted into the center of one comes out clean, about 20-25 minutes. Let the muffins cool completely in the pan before enjoying.
An overhead shot of crumble topped muffins set inside of a pink linen in a bowl. An apple is shown to the side.
22/09/2021 (Last Updated 09/05/2024)
Posted in: autumn, breakfast, dessert, nut free, snack, sweet, vegan, winter


5 from 16 votes (4 ratings without comment)

Recipe Rating

  • Laura

    5 stars
    I have an overflow of apples at the moment so decided to try out this recipe! I really liked that you stew the apples for a few minutes first with the cinnamon. Right before baking I realized I loaned out my muffin tin so I ended up baking this as a loaf for about 1 hour. It turned out great. The crumble top made it feel a bit more like a dessert!

    • Laura Wright

      Hi Laura!
      Thanks for letting us know how this worked as a loaf. I know that your comment will be helpful to folks in the future. Glad you enjoyed!

  • Amy

    5 stars
    These are delicious, even with half gluten-free white and half buckwheat flour for my gluten intolerant partner. I made chunky applesauce the night before (applesauce isn’t available in typical UK supermarkets) and used that instead of sautéing the apples on the day, which cut down a little on the somewhat hefty prep time. Worked great. Will be making these again!

  • Sandy

    5 stars
    These are absolutely the bomb! A little more work than expected but so well worth it. I used half AP Flour and half Whole wheat flour and it was perfect. Will be making again.

  • Susan

    5 stars
    These muffins were the perfect Saturday treat with hot tea! I didn’t manage to get all the crumble piled on but almost! I wouldn’t recommend any changes to this recipe, but I couldn’t help myself and added some vegan protein and inulin powder in place of some of the flour, in which I used half ap and half whole wheat. I think this made my muffins a bit softer, but nonetheless delectable.
    Thanks, I’m loving your website and I’m making brothy beans tonight!

  • Benjamin

    5 stars
    I love these muffins! They are my husband’s absolute favourite, especially in the fall. Question: How do people usually store them? I’ve tried both air-tight and lid askew containers but find the crispy topping gets a little soft. Is there a better way to store them to help keep the topping from going soft? They’re still really good, but I love them the most shortly after they’re out of the oven and the topping is nice and cripsy!

    • Laura

      Hey Benjamin,
      I would recommend wrapping them loosely in aluminum foil–this is what I usually do with coffee cake or other crumble-topped goods that I want to keep crisp.

  • Mate Mate PH

    5 stars
    Love this recipe and going to try lots of your recipes. 

  • Liz

    5 stars
    Hi Laura, I’m wondering if there’s an alternative to using lemon juice? I have a friend with a citrus allergy. 

    • Laura

      Hi Liz!
      You can leave the lemon zest out. The muffins will still be great without it :)

  • Vegan4life

    5 stars
    These muffins were delicious!  Everything I hoped they would be and maybe more. I made them pretty much exactly as written & baked for 25 minutes. Unsurprisingly the crumbly top is the best part, but the apple studded muffin base is remarkably good too! Even my skeptical kiddos loved them. Thanks for another great recipe, Laura! 

  • sadie

    These look lovely! I will give them a try. Question: Do you find that they freeze well? I have tween twins, and they are voracious! If these are freezer-friendly, I imagine I could stockpile them. ;) Thoughts? 

    • Laura

      Hi Sadie,
      These muffins freeze really well if they’re wrapped up nice and tight. Hope you love them!

  • Jessica

    Made these the day the recipe posted. They are fabulous! Perfect with the apples I just picked. Happy autumn!  

    • Laura

      Hi Jessica,
      I’m so glad that you enjoyed them. Happy Autumn to you as well :)

  • Marylynn Steckley

    5 stars
    Such a treat on this first autumn weekend! 

  • Miranda

    5 stars
    These are just lovely! I couldn’t quite get all the topping to fit on, but what stuck got perfectly crispy and crumbly. The apples melt right into the muffin, making them taste like apple pie – just a little less sweet.

  • Angela

    5 stars
    Delicious! Easy to make and not too sweet! I used coconut sugar for the batter (brown sugar for the topping still) and it was perfect! They smell amazing too. I will definitely add these muffins to my autumn baking rotation!

  • Kim Lippy

    5 stars
    QUESTION: Disclosure – I’ve not made this. Tell me please, how many sugars do these muffins have?