These vegan apple cranberry pecan muffins are my personal ode to fall. A moist and tender almond-oat crumb, pops of tart cranberry, warm apple throughout, and a candied maple pecan top that finishes everything off with a sweet crunch. Naturally gluten-free, no mixer, and ready in just 30 minutes.

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Ingredients for vegan apple cranberry pecan muffins
- Almond flour: the base providing a buttery and moist texture.
- Oat flour: combined with almond flour, it creates the perfect naturally gluten-free baking blend
- Baking powder and baking soda: both are needed for a rise and to ensure the muffins bake through evenly
- Salt: iodized, sea salt, or Himalayan all work well
- Plant-based milk: unsweetened flax, almond, or cashew work best. I love Califia Farms organic 3-ingredient options
- Apple cider vinegar: essential for creating the vegan buttermilk
- Apple: Fuji, Gala, Pink Lady, or Honeycrisp all work great, coarsely grated
- Maple syrup: naturally sweetens and acts as a binder
- Frozen cranberries: add the perfect burst of tart sweetness in each bite. Dried cranberries can be used in a pinch.
- Pecans: a must for a sweet and buttery crunchy topping
- Cane sugar: provides that nostalgic sugary muffin top and helps to almost carmalize the pecans
How to make gluten-free muffins
1. Preheat and prep
Preheat your oven to 350°F and line a muffin pan with large unbleached baking cups or lightly grease 10 of the 12 cavities.
2. Make the vegan buttermilk
Combine plant-based milk and apple cider vinegar in a small measuring cup or bowl and let it sit for 5 minutes. It will curdle slightly — this is exactly what we want.
3. Mix the dry ingredients
Add almond flour, oat flour, baking powder, baking soda, and salt to a large mixing bowl and stir to combine.
4. Add the wet ingredients
Grate the apple directly into the dry ingredients, then add the maple syrup and buttermilk. Stir until a thick batter forms. It will be similar to cookie dough texture.

5. Fold in the cranberries
Gently fold in the frozen cranberries and scoop the batter into the prepared muffin pan, filling each cup.
6. Add the sweet, nutty topping
Combine pecans, maple syrup, and cane sugar in a small bowl and spoon over each muffin. Add an optional sprinkle of cane sugar on each muffin. Bake for 20-23 minutes until the tops are golden, and a toothpick comes out mostly clean.

7. Cool and serve
Let the muffins cool for at least 10 minutes before eating. If desired, add a bit of vegan butter for an additional element of coziness.
Substitutions
- Almond flour: swap for cashew flour as a 1:1 replacement, or use 2 cups oat flour total for a nut-free version. The muffins will be slightly denser, and you may need a little extra milk (⅔ cup milk vs ½ cup). If the batter feels too dry, add a tablespoon more at a time. A spoonful of unsweetened applesauce also helps with moisture.
- Apple: Fuji and Gala are my go-tos, but Honeycrisp, Granny Smith, and Pink Lady all work well. No apple on hand? 1 cup of unsweetened applesauce works too. For a stronger apple flavor, dice instead of grating.
- Plant-based milk: an unsweetened variation works best so the other flavors can shine through. Use your favorite (almond, cashew, soy, oat, etc.)
- Apple cider vinegar: swap for lemon juice in a pinch. The flavor will be slightly different but it works.
- Frozen cranberries: Dried cranberries also work. The softer and stickier they are, the better. If they feel too stiff, soak them in orange juice for 10 minutes before adding them to the batter.
- Pecans: walnuts, hazelnuts, macadamia nuts, or slivered almonds all make good swaps. For a nut-free version, use thin apple slices on top instead.

Variations
- White chocolate: fold vegan white chocolate chips into the batter or finish with a drizzle of melted chocolate on top. To melt, combine chips and a small amount of coconut oil in a microwave-safe dish and heat in 30-second intervals, stirring between each. Pascha (bars and chips) and Enjoy Life Foods are certified gluten-free and vegan.
- Spiced: add ½ teaspoon cinnamon, ¼ teaspoon nutmeg, and a pinch of ginger to the dry ingredients for a warmer, spiced version. Good for deep fall or holiday baking.
How to store and reheat muffins
These muffins don't do well on the counter for more than a day — they soften, and the flavor starts to change. Store in the fridge for 3-5 days or in the freezer for up to a month.
To reheat, slice in half and place both halves face-down on a warm griddle or skillet until golden. If reheating from frozen, let them thaw at room temperature first.
Try these recipes next:
- Gluten-free and Dairy-free Blueberry Muffins
- Vegan White Chocolate Oatmeal Cranberry Cookies
- Homemade Chocolate Pecan Turtle Bites with Dates

📋 Recipe
Vegan Apple Cranberry Pecan Muffins
Equipment
- mixing bowl + spatula or wooden spoon
- measuring cup + spoons
- muffin pan + unbleached baking cups
Ingredients
Dry
- 2 cups almond flour, packed
- 1 cup gluten-free oat flour, packed
- 2 teaspoons baking powder
- 1 teaspoon baking soda
- ½ teaspoon iodized salt (or salt of choice)
Vegan buttermilk
- ½ cup + 1 tablespoon plant-based milk
- 1 tablespoon apple cider vinegar
Other wet ingredients
- ¼ scant cup maple syrup
- 1 cup coarsely grated apple 1 large apple or 2 smaller apples
- 1 cup frozen cranberries
Pecan Maple Topping
- ½ heaping cup chopped raw pecans
- 1 teaspoon cane sugar
- 2 tablespoons pure dark maple syrup
Additional topping (optional)
- sprinkle of cane sugar on each muffin top
Instructions
- Preheat oven to 350° F and line a muffin pan with large unbleached baking cups or lightly grease 10 of the 12 cavities.
- Add flax milk and apple cider vinegar to a glass measuring cup (or something similar) and let sit for 5 minutes.
- Add all dry ingredients to a medium-large mixing bowl and stir to combine.
- Grate the apple(s) directly into the dry ingredients using a coarse grater. Alternatively, grate onto a plate or bowl, then add directly into the dry ingredients. Add maple syrup and vegan buttermilk and stir to combine. Fold in cranberries. The batter should be thick, similar to cookie dough.
- Scoop the batter into prepared muffin pan, filling each cup. I used a large ice cream scoop (~5 tablespoons) but feel free to use a ¼ measuring cup or just spoon each until full. Combine pecans, maple syrup, and cane sugar in a small bowl and top each muffin with a spoonful. Add an additional sprinkle of cane sugar (optional but recommended).
- Bake on the middle rack for 20-23 minutes or until the tops are golden brown and a toothpick comes out mostly clean. Remove and let cool for at least 10-20 minutes.
Notes
- Packed flour: scoop your measuring cup directly into the bag and press firmly against the side of the bag as you drag it up, or pour flour in and pat down until level with the rim.
- Homemade oat flour: add GF rolled oats to a blender and blitz until a fine flour forms.
- Grating the apple: use the largest grating option on a box grater. If your grater only has smaller holes, dice the apple instead to keep some texture.
If you made these apple cranberry pecan muffins, let me know your thoughts (and customizations) in the comments below. xo, Morgan







Michael says
These muffins are fantastic! You continue to blow me away with V/GF recipes, keep up the great work.
Claire Panella says
Very good! Had to bake a little longer. loved them and healthy! Thank you
Morgan says
I'm so glad to hear you loved them, Claire! The note about the baking time is super helpful, so thank you for taking the time to leave a review - it's greatly appreciated! 💗