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Enjoy a taste of fall with these apple cider sourdough muffins. Apple cider muffins are sweet, tender and filled with apple flavor from the apple cider, fresh apple and applesauce. The combination of warm spices, sourdough discard and cinnamon sugar give these sweet muffins the perfect balance of flavor. Quick to whip up and easy to bake, these muffins can be on your table in 40 minutes. Perfect for a quick snack or to start your morning with a yummy breakfast, make these apple cider sourdough muffins today!

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Why You’ll Love Apple Cider Sourdough Muffins
- Apple Flavor: These muffins get their apple flavor from apple cider, apples, and applesauce. If you want a rich apple flavor in your muffins, make sure you’re using good-quality apples! Or try my delicious Sourdough Apple Cider Donuts for a mild-flavored fall favorite.
- Quick & Easy: These apple cider muffins only take 40 minutes from start to finish, and they are a great way to make use of fresh, seasonal apples.
- Discard Recipe: I love finding seasonal recipes that make use of sourdough discard, and the sourdough makes these sourdough apple cider muffins so so good – just like with these Spinach Sourdough Banana Muffins!

Important Ingredients
- Sourdough Discard: You can use fresh, bubbly sourdough starter if you want. If you don’t mind a more pronounced sourdough flavor, you can use refrigerated discard up to a week or two old. I always use 100% hydration sourdough discard.
- Sugar: Granulated sugar and brown sugar work together to give these muffins a sweet flavor. If you prefer a less sweet muffin, you can reduce the sugar by a few Tablespoons.
- Flour: All-purpose flour works well for this recipe. I use an all-purpose flour with 11.5% protein content.
- Spices: Ground cinnamon and nutmeg are used to enhance the flavor of the apple in these apple cider sourdough muffins.
- Eggs: Eggs bring richness, a good texture and help muffins rise.
- Greek Yogurt: Gives these muffins a tender crumb and keeps them moist. You can substitute sour cream if desired.
- Vegetable Oil: Any neutral-flavored oil works well in this recipe. You can also substitute melted butter if desired.
- Apple Cider: Apple cider is typically 100% apple juice (not made from concentrate). Store-bought “apple juice” is often made from concentrate. You can use apple juice in these muffins, but they won’t have the same apple flavor in them as fresh apple cider has. Be sure to save some cider to drink with your muffins!
- Apples: Choose a flavor-forward apple. My favorites are honey crisp, pink lady and granny smith.
- Applesauce: I prefer unsweetened applesauce in this recipe. Homemade or store-bought both work well.

How to Make Sourdough Apple Cider Muffins
Mixing Together Muffin Batter
Dry Ingredients: In a medium-sized bowl, whisk together the flour, baking soda, cinnamon, nutmeg and salt. Grate the apple and add on top of the dry ingredients. Fluff together.
Liquid Ingredients: Mix together the sourdough discard, brown sugar, white sugar and eggs. The discard will loosen up and start to combine with the sugars and egg. Add the yogurt, applesauce, oil, apple cider and vanilla extract. Whisk together until combined.
Mix together: Add the liquid ingredients to the top of the dry ingredients and stir until just combined with just a few dry streaks remaining. Be careful not to over-mix the batter. The less gluten that develops, the more light and tender the muffins will be.



Sprinkle Muffin Tops with Cinnamon Sugar
Prepare a 12-cup muffin tin with cooking spray, lining them with parchment squares or using muffin cups (spray the cups!). Put a scoop of batter in each tin, about 2/3 of the way full. Each cup can be used as this recipe makes 12-14 muffins. Generously sprinkle a cinnamon/sugar mixture over the tops of the muffins. This cinnamon/sugar mixture gives a crunchy and sweet muffin top texture.



Baking Apple Cider Sourdough Muffins
Put the muffins in a preheated 375°F oven and bake for about 20-22 minutes. Be careful not to open the oven door while the muffins bake. Stick a toothpick in the center of a muffin to check for doneness and remove from the oven when baked through. Let cool for 5-10 minutes in the muffin tin before removing to a cooling rack. Enjoy!


Substitutions
You can substitute apple juice for apple cider BUT the muffins will not have as much apple flavor. They will still be tender and delicious, just not quite the same apple flavor that fresh apple cider brings.


How to Store Leftovers
Leftover muffins can be stored at room temperature in an airtight container for a few days. If you plan to keep them longer than that, freeze any unused muffins for up to a few months.
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Frequently Asked Questions
Let muffins cool completely before storing in an airtight container or ziplock bag. I freeze extra muffins for up to 2 months.
You can, BUT the muffins will not have as much apple flavor. They will still be tender and delicious, just not quite the same apple flavor that fresh apple cider brings.
I prefer this recipe with grated apple. The apple melts into the muffins instead of being a chunk of apple. If you prefer apple chunks, you can use those instead. If you really like chunks of apple, check out my sourdough discard apple cake.

Apple Cider Sourdough Muffins
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Equipment
Ingredients
- 250 grams all-purpose flour, about 1 2/3 cup
- 6 grams baking soda, 1 teaspoon
- 8 grams salt, 1 teaspoon
- 4 grams ground cinnamon, 1 1/2 teaspoons
- 1 gram nutmeg, 1/2 teaspoon
- 100 grams sourdough discard, 100% hydration, see recipe notes
- 70 grams granulated sugar, about 1/3 cup
- 70 grams brown sugar, about 1/3 cup
- 2 large eggs, about 100 grams total
- 65 grams plain Greek yogurt, about 1/3 cup
- 65 grams unsweetened applesauce, about 1/4 cup
- 50 grams vegetable oil, about 1/4 cup, any neutral-flavored oil works
- 75 grams apple cider, about 1/3 cup, see recipe notes
- 4 grams vanilla extract, about 1 teaspoon
- 120 grams grated apple, about 3/4 -1 cup, see recipe notes
- cinnamon/sugar for sprinkling, see recipe notes
Instructions
- Preheat oven to 375°F.
- To a medium-sized bowl whisk together the flour, baking soda, cinnamon, nutmeg and salt. Whisk to combine.
- Grate an apple. Add the grated apple to the flour mixture and fluff to combine.
- To a liquid measuring cup or small bowl, add sourdough discard, brown sugar, white sugar and eggs. Whisk together until combined and the sourdough discard incorporates with the sugar and eggs. Then add the yogurt, applesauce, oil, apple cider and vanilla extract. Whisk together until combined.
- Pour the liquid ingredients on top of the dry ingredients and mix until just combined.
- Spray a 12 cup muffin tin with cooking spray or line with parchment papers. If you use baking cups, spray them so the muffins come out easily. Scoop about 2/3 cup batter in each pocket.
- Generously sprinkle granulated sugar and cinnamon over the top of every muffin.
- Bake muffins for 20-22 minutes at 375°F. Once baked all the way through, pull out of the oven and let cool for 5-10 minutes before removing to a baking rack. Enjoy!
Notes
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.




Could you make this into one big bread loaf? I can’t find my muffin tins anywhere!
I would probably make this Sourdough Apple Bread recipe if I didn’t have muffin tins. Good luck!
I made these they came out great is there an option to replace the yogurt for nondairy
Thanks
This recipe doesn’t have a non-dairy substitute suggestion. You can try leaving it out and increasing some of the other liquid ingredients to compensate. You can also try this recipe for sourdough apple bread that doesn’t contain dairy instead (sub the butter in that recipe for a different oil to make it fully dairy free). Hope that helps!
These look amazing!! I live in a small town and can’t get apple cider locally. I’m assuming apple juice would be ok to sub… would you adjust any other ingredients to add move flavor?
I’m sorry apple cider isn’t readily available where you live. You can definitely use apple juice instead. Unfortunately, it won’t have as strong of flavor as using apple cider, but your muffins will still be tender and delicious!
Could these be made into mini loaves of bread instead of muffins? Would the cook time differ?
I think you could do that. I would probably bake for 25-30 minutes in the mini loaf tins.
I just pulled the mini loaves out of the oven 12 minutes ago, and couldn’t wait to try them! Absolutely delicious, I made 4 mini loaves, and they baked for 27 minutes. I have tried several of your recipes, and have loved them all!
So glad it worked well! Thanks for letting me know 🙂
I made these the other day and they were very good! I just loved them. Goingon my Christmas morning brunch. Thank you for all tour reat recipes!
So glad you loved this recipe!
Loved these, the flavor is not overwhelming but very fall like and nice texture. Mine made more than 12, about 15 in standard size muffin pan.
So glad you enjoyed this recipe! Thanks for sharing.
These were delicious, not too sweet, and my little grandchildren loved them. That’s a win in my book!
Love this! So glad you loved these 🙂
Yes, I used my mini cupcake pan to make a dozen minis that the grandchildren enjoyed.
Just made these and they came out great! I cut my apple into small cubes and then made a crumb topping with some small apple pieces. So far they’re a hit! Thank you!
So glad you enjoyed them! Thanks for sharing.
Do these freeze well?
Yes. Very well.
Is there something I could substitute for the applesauce?
I have every other ingredient. I don’t want to have to run out for applesauce.
You could sub oil instead of the applesauce.
What an interesting recipe! Can’t wait to try it! 😍🍎🍏🧁🍂🍁