There’s just something magical about the combination of sourdough, cinnamon, and apples when the weather starts to cool down. These Sourdough Discard Apple Cinnamon Roll Muffins are a fall-inspired twist on my beloved Sourdough Discard Cinnamon Roll Muffins, the recipe so many of you have fallen in love with!
They have everything you adore about the original: the soft, tender crumb, the gooey cinnamon swirl, and that irresistible bakery-style topping. But this time, we’re adding sweet spiced apples that make every bite taste like a cozy fall morning. Warm from the oven and drizzled with an optional caramel glaze, these muffins are pure autumn comfort!
Why I love this recipe
- Same-Day Bake – No need for an overnight rise! These muffins come together quickly, making them perfect for a spontaneous sweet treat.
- Soft, Fluffy, and Irresistible – The muffins bake up light, airy, and perfectly tender, with gooey cinnamon swirls in every bite.
- A Delicious Way to Use Up Sourdough Discard – Instead of throwing away extra starter, this recipe puts it to good use, adding flavor and texture to the dough.
Tips for success
- If the dough feels sticky, add a tablespoon or two of extra flour or chill it for 15–20 minutes before rolling it out — this makes it much easier to handle.
- Flour your work surface and rolling pin well to prevent sticking and keep the dough smooth while rolling.
- Dice the apples finely so they bake evenly and tuck nicely into the cinnamon swirl. I love using this vegetable chopper for easy and even dicing!
- Use crisp baking apples like Honeycrisp, Pink Lady, or Fuji for the best texture and flavor.
- Bake until golden and set in the center; underbaking can make the bottoms gummy.
How to make sourdough discard apple cinnamon roll muffins: step-by-step
Can I long ferment the dough? Yes! Just mix all the ingredients together, knead the dough into a smooth (ish) ball, cover it, and refrigerate overnight — it’ll be ready to shape and bake the next day.
Ingredients
- 150 grams sourdough discard (no more than a week old & room temp)
- 50 grams sugar
- 55 grams milk (warmed)
- 120 grams full fat sour cream or full fat Greek yogurt
- 1 large egg
- 1 tsp vanilla extract
- 30 grams unsalted butter (softened)
- 360 grams all-purpose flour
- 1 teaspoon baking powder
- 1/2 teaspoon baking soda
- 5 grams salt
Cinnamon sugar base layer
- 70 grams softened unsalted butter
- 60 grams brown sugar
- 1 & 1/2 teaspoons cinnamon
Apple Cinnamon Filling
- 3 medium or 2 large apples peeled and diced small (1/4 inch cubes)
- 25 grams (2 tablespoons) unsalted butter
- 40 grams (3 tablespoons) light brown sugar
- 1 teaspoon cinnamon
- 1/4 teaspoon nutmeg
- Pinch of salt
- 1 teaspoon lemon juice (optional, brightens flavor)
- 2 teaspoons cornstarch + 2 teaspoons water (slurry to thicken the filling)
Crumble Topping
- 57 grams melted unsalted butter
- 25 grams sugar
- 25 grams brown sugar
- 70 grams flour
- 1/2 teaspoon ground cinnamon
- a pinch of salt
Caramel Glaze (optional)
- 75 grams brown sugar
- 45 grams unsalted butter
- 20 grams heavy cream
- pinch of salt
Equipment
- Mixing bowl
- Bench/dough scraper
- Rolling Pin
- Food scale/measuring spoons
- 12 cup muffin pan
- Muffin liners (optional but handy!)
Instructions
The sourdough discard brioche dough can be mixed by hand or a stand mixer.
- Warm the milk in the microwave for 30–45 seconds, then add it to a mixing bowl with the sour cream (or Greek yogurt) and stir until the mixture is smooth and well combined.
- Stir in the sourdough discard and sugar until mostly dissolved. Then whisk in the egg and vanilla extract.
- To a separate bowl whisk together the flour, baking soda, baking powder, & salt, and slowly add it to the wet mixture along with the softened butter.
- Mix until the ingredients come together into a shaggy dough, then cover and let it rest for 20–30 minutes to hydrate and relax.
- After resting, knead the dough until it becomes fairly smooth, being careful not to add too much extra flour, as this can alter the final texture. It should remain slightly sticky even after kneading.
- Once complete, cover the dough and let it rest for another 15-30 minutes.
Make the apple filling & crumble topping
For the apple filling
- Melt the butter in a skillet over low-medium heat. Add the diced apples, brown sugar, cinnamon, nutmeg, and salt. Cook 4-5 minutes until softened, but not mushy.
- Stir in the lemon juice (if using) and corn starch slurry and cook briefly until the mixture has thickened.
- Cool completely before using.
I love this vegetable chopper for effortless dicing!!
For the crumble topping:
- In a small bowl, combine cooled melted butter, both sugars, cinnamon, salt, and flour. Mix until crumbly and chill until ready to use. If the mixture is too wet add a little more flour. If it is too dry. add a little more melted butter.
Shaping sourdough discard apple cinnamon roll muffins
- Line a 12 cup muffin pan with muffin liners and preheat the oven to 350 degrees F.
- Mix the cinnamon sugar base layer: mix together the softened butter, brown sugar, and cinnamon until a paste is formed.
- After resting, roll the dough out on a lightly floured surface into a 20×10-inch rectangle. Tip: flour your rolling pin to avoid it from sticking.
- Spread the cinnamon sugar base layer on the surface of the dough leaving a 1/2-inch border. Then scatter the apple filling across evenly and press gently to adhere.
- Using a ruler or visually estimating, lightly score the top of the dough every 1.5 inches to help guide the cuts and maintain uniformity. Use a pizza cutter to make clean, straight cuts through the dough. You will end up with 12 muffins total.
- Roll each apple cinnamon roll individually as tight as possible to keep all the filling in and place each one into the muffin pan. These rolls are a bit thicker and may need to be gently pressed into each muffin cup to fit.
- Sprinkle the crumble topping generously over each roll and bake for 28-32 minutes or until the internal temperature reads 190-200 degrees F.
- Allow the sourdough discard apple cinnamon roll muffins to rest for 10-15 minutes before removing from the pan.
- While they rest make the optional caramel glaze.
Make the caramel glaze
- In a small saucepan, melt the butter and brown sugar together. Stir in the heavy cream and simmer 1-2 minutes until smooth. Remove from heat and stir in the pinch of salt. Let cool sightly to thicken.
- If the glaze thickens too much add a splash of milk to thin it out.
- Generously glaze each cooled apple cinnamon roll muffin and enjoy!
- Sourdough discard Apple cinnamon roll muffins last for 2-3 days on the counter in an airtight container or 5 days in the refrigerator.
More sourdough discard fall recipes
- Apple Cinnamon Sourdough Scones (w/ a caramel glaze!)
- Sourdough Applesauce Cake
- Apple Cider Sourdough Donut Muffins
- Amish Apple Cider Donut Bread
Sourdough Discard Apple Cinnamon Roll Muffins
These sourdough discard apple cinnamon roll muffins are soft, gooey, and filled with warm spiced apples, an easy fall bake that tastes just like homemade cinnamon rolls.
Servings: 12 muffins
Equipment
- Mixing bowl
- Bench/dough scraper
- Rolling Pin
- Food scale/measuring spoons
- 12 cup muffin pan
- Muffin liners optional but handy!
Ingredients
For the dough
- 150 grams sourdough discard no more than a week old & room temp
- 50 grams sugar
- 55 grams milk
- 120 grams full fat sour cream or Greek yogurt
- 1 large egg
- 1 teaspoon vanilla extract
- 30 grams unsalted butter softened
- 360 grams all-purpose flour
- 1 teaspoon baking powder
- 1/2 teaspoon baking soda
- 5 grams salt
Cinnamon sugar base layer
- 70 grams unsalted butter softened
- 60 grams brown sugar
- 1 & 1/2 teaspoons ground cinnamon
Apple cinnamon filling
- 3 medium or 2 large apples peeled and diced small (1/4 inch cubes)
- 25 grams unsalted butter
- 40 grams light brown sugar
- 1 teaspoon cinnamon
- 1/4 teaspoon nutmeg
- pinch of salt
- 1 teaspoon lemon juice optional , brightens flavor
- 2 teaspoons cornstarch & 2 teaspoons water slurry to thicken the filling
Crumble Topping
- 57 grams unsalted butter melted
- 25 grams sugar
- 25 grams brown sugar
- 70 grams flour
- 1/2 teaspoon ground cinnamon
- a pinch of salt
Caramel Glaze
- 75 grams brown sugar
- 45 grams unsalted butter
- 20 grams heavy cream
- pinch of salt
Instructions
- The sourdough discard brioche dough can be mixed by hand or a stand mixer.
- Warm the milk in the microwave for 30–45 seconds, then add it to a mixing bowl with the sour cream (or Greek yogurt) and stir until the mixture is smooth and well combined.
- Stir in the sourdough discard and sugar until mostly dissolved. Then whisk in the egg and vanilla extract.
- To a separate bowl whisk together the flour, baking soda, baking powder, & salt, and slowly add it to the wet mixture along with the softened butter.
- Mix until the ingredients come together into a shaggy dough, then cover and let it rest for 20–30 minutes to hydrate and relax.
- After resting, knead the dough until it becomes fairly smooth, being careful not to add too much extra flour, as this can alter the final texture. It should remain slightly sticky even after kneading.
- Once complete, cover the dough and let it rest for another 15-30 minutes.
Make the apple filling & crumble topping
- For the apple filling: Melt the butter in a skillet over low-medium heat. Add the diced apples, brown sugar, cinnamon, nutmeg, and salt. Cook 4-5 minutes until softened, but not mushy.
- Stir in the lemon juice (if using) and corn starch slurry and cook briefly until the mixture has thickened. Cool completely before using.*The filling can be prepared the night before and refrigerated before using for flexibility.
- For the crumble topping: In a small bowl, combine cooled melted butter, both sugars, cinnamon, salt, and flour. Mix until crumbly and chill until ready to use. If the mixture is too wet add a little more flour. If it is too dry. add a little more melted butter.*The crumble can be prepared the night before and refrigerated before using for flexibility.
Shaping sourdough discard apple cinnamon roll muffins
- Line a 12 cup muffin pan with muffin liners and preheat the oven to 350 degrees F.
- Mix the cinnamon sugar base layer: mix together the softened butter, brown sugar, and cinnamon until a paste is formed.
- After resting, roll the dough out on a lightly floured surface into a 20×10-inch rectangle. Tip: flour your rolling pin to avoid it from sticking.
- Spread the cinnamon sugar base layer on the surface of the dough leaving a 1/2-inch border. Then scatter the apple filling across evenly and press gently to adhere.
- Using a ruler or visually estimating, lightly score the top of the dough every 1.5 inches to help guide the cuts and maintain uniformity. Use a pizza cutter to make clean, straight cuts through the dough. You will end up with 12 muffins total.
- Roll each apple cinnamon roll individually as tight as possible to keep all the filling in and place each one into the muffin pan. These rolls are a bit thicker and may need to be gently pressed into each muffin cup to fit.
- Sprinkle the crumble topping generously over each roll and bake for 28-32 minutes or until the internal temperature reads 190-200 degrees F.
- Allow the sourdough discard apple cinnamon roll muffins to rest for 10-15 minutes before removing from the pan. While they rest make the optional caramel glaze.
Make the caramel glaze
- In a small saucepan, melt the butter and brown sugar together. Stir in the heavy cream and simmer 1-2 minutes until smooth. Remove from heat and stir in the pinch of salt. Let cool sightly to thicken.
- If the glaze thickens too much add a splash of milk to thin it out.
- Generously glaze each cooled apple cinnamon roll muffin and enjoy!
- Sourdough discard Apple cinnamon roll muffins last for 2-3 days on the counter in an airtight container or 5 days in the refrigerator.
Notes
Can I long ferment the dough? Yes! Just mix all the ingredients together, knead the dough into a smooth (ish) ball, cover it, and refrigerate overnight — it’ll be ready to shape and bake the next day.
Can I use active starter? Yes recently fed or unfed starter can be used.
Use crisp baking apples like Honeycrisp, Pink Lady, or Fuji for the best texture and flavor.
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