The BEST Fresh Milled Sourdough Apple Pie Muffins
Enjoy the classic flavors of apple pie in these fresh milled sourdough apple pie muffins!
These delicious muffins will make the whole family very happy! Soft, flavorful, and so comforting, you will be making these over and over!

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In my opinion, nothing goes together like sourdough and fresh milled flour. In fact, I am very passionate on the subject!
Fresh Milled flour has so many well documented health benefits over all purpose flour. I find it to be so much more flavorful and satisfying!
Making your favorite sourdough recipes with fresh milled flour can be a bit tedious, however with muffins, you can easily make this sourdough recipe with whole grains with no learning curve!
These muffins can be made long fermented or quickly with sourdough discard.

Why I love this recipe
Easy – This is a super easy recipe to whip up as a nutritious and delicious snack for the kids!
Wholesome – Made with simple ingredients and free from refined sugar, these muffins are full of nutrition.
Delicious – The flavors in these fresh milled sourdough apple pie muffins are comforting like a slice of apple pie!
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To mill my own wheat, I use the Nutrimill Grain Mill.
I use the USA pan muffin tin.
For my favorite sourdough bread recipe, Click here!
For another sourdough muffin recipe, try my Sourdough Chocolate Chip Muffins
Ingredients you will need to make these fresh milled sourdough apple pie muffins
- Fresh Milled Flour – I used fresh milled Einkorn for these muffins. You can use hard white wheat, hard red wheat, soft white wheat, or spelt. You could also use whole wheat flour from the store.
- Salt
- Baking soda
- Baking Powder
- Sourdough Starter – For best results, when making the long fermented version, use active starter. Sourdough discard can be used with the quick method.
- Egg
- Grated Apples – Use crisp apples for the best result. My favorite are pink lady or granny smith apples.
- Milk
- Olive Oil – May also use melted butter or vegetable oil.
- Maple Syrup/Honey
- Vanilla Extract
- Cinnamon
- Nutmeg
- Millet (optional) – While this is an optional ingredient, I highly recommend it. Millet adds a delightful crunch to the muffins!
For full ingredient amounts, see recipe card below
For more of my sourdough recipes, Click here!

How to make fresh milled sourdough apple pie muffins
Long fermented method
The night before, in a large mixing bowl, add the flour, starter, and milk.
Mix well. Cover with plastic wrap and let the batter ferment at room temperature for 8-12 hours.
Note: If you are uncomfortable leaving the mixture out because of the milk, make the batter earlier in the day and let ferment in the fridge for at least 18 hours before proceeding.
The next morning, in a separate bowl, add the remainder of the ingredients and mix well.
Preheat the oven to 400 degrees F.
I use a box grater to grate my fresh apples. You will need 1 cup.
Pour the remaining mixed ingredients over the fermented batter and mix well.
Prepare a 12 cup muffin tin by spraying with a bit of oil or lining with either paper liners or silicone cupcake liners.
Evenly scoop the muffin batter into the muffin pan.
Bake for 15-17 minutes or until a toothpick placed in the center of the muffin comes out clean. They will be lightly golden brown.
Allow muffins to cool completely on a wire rack before storing.

Quick method made with Discard
Preheat the oven to 400 degrees F.
In a large bowl add the dry ingredients and mix well.
Grate the fresh apples using a box grater. You will need 1 cup.
In a separate bowl combine the wet ingredients and mix well.
Pour wet ingredients over the flour mixture and mix well.
Prepare a 12 cup muffin pan by spraying the muffin cups with oil or using muffin liners.
Evenly scoop the batter into the muffin pan.
Bake for 15-17 minutes or until a toothpick placed in the center of the muffin comes out clean. They will be lightly golden brown.
Allow muffins to cool completely on a wire rack before storing.
Storage Tips
Store leftover muffins in a plastic bag or airtight container on the counter for 3-4 days.
Freeze muffins in a freezer bag for up to 3 months.


Fresh Milled Sourdough Apple Pie Muffins
Equipment
- 12 cup muffin tin
Ingredients
- 2 1/2 cups fresh milled flour I used Einkorn
- 1 tsp salt
- 1 tsp baking powder
- 1 tsp baking soda
- 1/2 cup sourdough starter
- 1/2 cup milk
- 1/4 cup maple syrup or honey
- 1/4 cup olive oil
- 1 cup shredded apple
- 1 egg
- 1 tsp vanilla extract
- 2 tsp cinnamon
- 1/2 tsp nutmeg
- 1/4 cup millet optional (for crunch)
Instructions
For Long Fermented
- The night before, add the flour, starter, and milk to a large bowl and mix well.
- This will be a thick batter. Cover and let ferment on the counter for 8-12 hours.
- The next morning, preheat the oven to 400 degrees F.
- Grate 1 cup of apples.
- Add the apples and the remaining ingredients to the fermented mixture.
- Mix well and scoop equally into a 12 cup muffin tin that has been sprayed with oil or lined with muffin liners.
- Bake in preheated oven for 15-17 minutes or until a toothpick comes out clean.
- Allow to cool on wire rack before storing.
For quick method with Discard
- Preheat oven to 400 degrees F.
- In a large bowl, mix the flour, baking soda, baking powder, salt, cinnamon, and nutmeg. Mix well.
- In a separate bowl, add the starter, milk, oil, maple syrup or honey, vanilla extract, egg, and grated apple.
- Mix well and pour into the dry ingredients.
- Mix until combined. Optionally, add in the millet.
- Prepare a 12 cup muffin tin by adding some oil or muffin liners.
- Scoop the batter evenly into the muffin tin.
- Bake for 15-17 minutes or until a toothpick comes out clean.