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Vegan Apple Crisp Muffins

5 from 9 votes
Prep Time 15 mins
Cook Time 30 mins
Total Time 45 mins
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


  • 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.

Recipe Notes

  • 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.
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.