These Fresh-Milled Sourdough Apple Cinnamon Muffins are a delicious, healthy treat made with freshly milled soft white wheat and einkorn. The combination creates a wonderfully tender muffin with the added flavor and nutrition of whole grains. They’re especially lovely in the fall, when fresh apples are in season and cozy baking is at its best.
Warm cinnamon and sweet apples fill the kitchen with an irresistible aroma as the muffins bake, giving your home that wonderful cozy fall feeling! Sourdough discard adds a subtle depth of flavor while helping create a soft, tender crumb. Easy to make and completely dairy-free, these muffins are perfect for breakfast, an afternoon snack, or sharing with family and friends.

Why You’ll Love This Recipe
This recipe is super easy to make and very flexible for timing. It makes 18 muffins, so plenty to freeze and have homemade fresh-milled muffins at a moments notice. They are also a wonderful way to use up any extra sourdough discard you have on hand.
You can bake the muffins the same day you make the batter or let it sit in the fridge overnight to develop flavor and save time in the morning.
If you love these muffins – be sure to check out my Fresh-Milled Sourdough Blueberry Muffins or my Fresh-Milled Sourdough Chocolate Chip Muffins. Or if you’re in the mood for banana bread instead, checkout my Fresh-Milled Sourdough Banana Bread. For another delicious fall treat made with fresh apples, you will love my Fresh-Milled Apple Cinnamon Scones.

Tips for Success
- Make sure you weigh your wheat berries before milling. This ensures that you will have the correct amount of flour for the recipe. If you measure one cup of wheat berries, you will end up with more flour than you need.
- Mill your wheat berries on the finest setting that your grain-mill allows. You will have the most tender muffins with fine flour.
- Don’t skip the 15 minute rest! This gives the fresh-milled flour time to absorb the liquids before baking. Whole grain flour absorbs water more slowly than all purpose flour does, so it needs a little extra time. This is why I really love letting the batter sit in the fridge overnight if possible.
Storage & Freezing
These muffins can be stored at room temperature for 3 – 4 days. For best results, I recommend freezing them. If you have the freezer space, place the fresh baked muffins on a baking sheet and place in the freezer for several hours. Then transfer them to a freezer bag for long term storage – up to 6 months.
Reheating Frozen Muffins
Reheat the frozen muffins in the oven at 325 degrees F for about 12 minutes. They will be just as soft and delicious as they were when they were first baked!
Please Share!
If you like this recipe, please share it anyone that you think might be interested. This really helps to get my recipes seen by people that will enjoy them! If you have any questions, I’m happy to help as always. Just leave a comment below!

Fresh-Milled Sourdough Apple Cinnamon Muffins
Equipment
- 1 Kitchen Scale
- 1 12 Hole Muffin Pan
- 1 6 Hole Muffin Pan
- 1 Muffin Scoop optional
Ingredients
- 255 g soft white wheat berries
- 120 g einkorn berries
- 5 g salt
- 2 tsp baking powder
- 1/2 tsp baking soda
- 2 1/4 tsp ground cinnamon
- 120 g apples cut in cubes
- 100 g sourdough discard
- 150 g cane sugar
- 113 g avocado oil
- 3 large eggs room temperature
- 177 g applesauce
- 2 tsp vanilla extract
Instructions
- Finely mill the wheat berries into a medium bowl.255 g soft white wheat berries, 120 g einkorn berries
- Add the salt, baking powder, baking soda, and ground cinnamon to the freshly milled flour. Whisk to combine.5 g salt, 2 tsp baking powder, 1/2 tsp baking soda, 2 1/4 tsp ground cinnamon
- Add the apples and toss to coat in the flour.120 g apples

- To a large mixing bowl, add the sourdough discard, sugar, avocado oil, eggs, applesauce, and vanilla extract. Whisk to combine.100 g sourdough discard, 150 g cane sugar, 113 g avocado oil, 3 large eggs, 177 g applesauce, 2 tsp vanilla extract

- Add the flour with apples to the wet ingredients and gently stir until no dry flour remains in the bowl.

- Cover the bowl and let the batter rest for 15 minutes.
- Preheat your oven to 400℉ and line the muffin pans with parchment liners.
- Scoop the batter into the muffin pans and bake for 8 minutes. Then turn the oven temperature down to 350℉ and bake for an additional 12 minutes until lightly golden brown. A toothpick inserted in the middle of a muffin should come out clean.

- Cool the muffins in the pan for 5 minutes before transferring to a wire rack to cool completely.








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