Sourdough Apple Pie Cupcakes with Fresh Milled Flour
These Sourdough Apple Pie Cupcakes made with Fresh Milled Flour are irresistible and will be your go-to treat this season. If you bake sourdough, you know that discard can pile up. Rather than toss it, fold it into your cupcake batter to add a gentle tang, more moisture, and a lovely texture. It’s not going to make them into sourdough bread, so don’t worry!
So get your grain mill (or fresh flour), your sourdough discard, and your apple pie filling ready. Let’s bake a cozy, flavorful batch that’s part pie, part cupcake, and part sourdough magic.
Try making more delicious muffins this season, like cozy Pumpkin & Pecan Muffins, Sourdough Chocolate Chip Muffins, or Apple Cider Mini Muffins. For more fall bakes, check out our Favorite Fall Sourdough Recipe Roundup, which includes Apple Pie Oat Bars, Sourdough Apple Pie Cobbler, and Sourdough Discard Pumpkin Bread.
Other fun desserts and staples include Whole Grain Pie Crust, Pecan Pie Bars, Krum Kake Cookies.
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Why You’ll Love These Apple Pie Cupcakes with Discard
Fresh milled whole grains bring a subtle nuttiness and heartiness without the heft to these cupcakes. The discard contributes a mild tang and depth you don’t get in regular flour desserts.
Sweet apple pie filling and sour cream keep these cupcakes extra moist with a tender crumb. It’s familiar but elevated; classic apple pie, cinnamon, and buttery frosting — but with a fresh twist.
Sourdough Discard Apple Pie Cupcake Recipe
Tools
- Grain Mill
- Mixing Bowls
- Danish Whisk
- Muffin Pans
- Paper Liners (or grease)
- Small Saucepan
- Spatula
- Piping bag + tip (optional)
- Thermometer
- Cooling Rack
- Kitchen Scale
- Hand Mixer
Cupcake Ingredients
- 113 grams Butter, melted
- 110 grams Sourdough Discard
- 1 Egg, room temperature
- 180 grams Sour Cream
- 5 grams Vanilla Extract
- 250 grams Soft White Wheat
- 200 grams Sugar
- 10 grams Baking Powder
- 3 grams Baking Soda
- 1/2 tsp Cinnamon
- 400 grams Diced Apple Pie Filling
Cinnamon Cream Cheese Frosting
- 115 grams Cream Cheese, softened
- 60 grams Butter, softened
- 80 grams Brown Sugar
- 56 grams Milk (or cream)
- 1 tsp Vanilla Extract
- 1 tsp Cinnamon
- Pinch of Salt
Notes:
- This recipe usually makes 18 cupcakes (when batter is filled about 2/3 full)
- This batter texture will be similar to muffin batter and/or cake batters
- You can make the frosting the day before and keep it in the fridge until ready to frost, just re-whip before piping
- If you like more frosting coverage on your cupcakes, you may want to double the frosting recipe
Apple Pie Filling
We make and can our own homemade apple pie filling each fall when the apple harvest comes in. If you don’t have any on hand, you can make some using the recipe below. If you are not using pre-made or home-canned apple pie filling, make this first and then be sure to fully cool it before adding 400 grams to the recipe.
Ingredients
- 4 Medium Apples (Fuji, Honeycrisp, Gala, Granny Smith apples), peeled, cored, and diced
- 60 grams Butter
- 100 grams Brown Sugar
- 2 tsp Cinnamon
- Pinch of Salt
- 1 Tbsp Flour or Cornstarch
Instructions
Prep: Peel, core, and dice apples.
Cook: Melt butter in a saucepan over medium heat. Add in diced apples and cook for a few minutes. Add in brown sugar, cinnamon, and salt. Continue to cook for another 4-5 minutes, or until the sauce is shiny and apples have softened. Whisk in cornstarch or flour and cook for 3-5 minutes, or until thick.
Step-by-Step Apple Pie Cupcakes
Preheat and Prep: Preheat your oven to 400°F and line muffin pan(s) with liners or grease.
Wet Ingredients: In the large bowl, whisk together melted butter, sourdough, sour cream, egg, vanilla, and sugar until smooth.
Dry Ingredients: Mill your wheat into the wet ingredients and then add baking powder, baking soda, salt, and cinnamon.
Combine: Gently fold the flour mixture and wet ingredients together. Then slowly fold in the apple pie filling.
Fill and Rest: Fill cupcake liners about 2/3 full of batter and let rest on the counter for 5-10 minutes.
Bake and Cool: Bake for about 15 minutes, or until internal temp is 200°F. Let cupcakes rest in the pan 5 minutes, then transfer to a wire rack to cool fully.
Frosting: While cupcakes are baking make the frosting. Melt and whisk brown sugar and milk in a saucepan over medium heat for 3-5 minutes, remove from heat, add vanilla and salt, then let it cool.
In a small mixing bowl, beat softened cream cheese and butter, and cinnamon until smooth. Slowly add the cooled, melted sugar mixture while using a hand mixer to beat until a fluffy consistency is reached. Cover and place in fridge for 30-60 minutes.
Frost Cupcakes: Once cupcakes are fully cooled, frost with a piping bag if desired, or spread on with a knife. Optionally, top with a dusting of cinnamon or a tiny dice of fresh apple.
Tips for Sourdough Apple Pie Cupcakes
- Don’t expect discard to replace your leavening agents. It adds flavor and texture, not lift — so don’t leave out the baking powder or soda.
- Be gentle mixing. This recipe prefers gentle handling, as overmixing can lead to toughness.
- Let the batter rest before baking. 5–10 minutes resting after you combine and scoop the batter can help the flour hydrate fully and reduce dryness.
Variations & Twists
I love eating these as the recipe is, but I also enjoy trying to mix it up every once in a while. Make a Salted Caramel to drizzle over the frosting or try a Streusel Crumble Topping + No Frosting — combine oats, butter, brown sugar, cinnamon, and sprinkle on batter before baking.
You could make an adult version by adding a tablespoon of bourbon or apple brandy to the apple filling or turn these into mini cupcakes — bake in mini liners and reduce the bake time!
You love these special treats for your family, potlucks, or parties. Full disclosure, I end up eating two of these myself before I even share!
Sourdough Apple Pie Cupcakes with Fresh Milled Flour
Bake cozy apple pie cupcakes using fresh milled flour and sourdough discard. Step-by-step recipe, tips, & icing recipe inside.
Ingredients
Cupcake Ingredients
- 113 grams Butter, melted
- 110 grams Sourdough Discard
- 1 Egg, room temperature
- 180 grams Sour Cream
- 5 grams Vanilla Extract
- 250 grams Soft White Wheat
- 200 grams Sugar
- 10 grams Baking Powder
- 3 grams Baking Soda
- 1/2 tsp Cinnamon
- 400 grams Diced Apple Pie Filling
Cinnamon Cream Cheese Frosting
- 115 grams Cream Cheese, softened
- 60 grams Butter, softened
- 1 tsp Cinnamon
- 80 grams Brown Sugar
- 56 grams Milk (or cream)
- 1 tsp Vanilla Extract
- Pinch of Salt
Apple Pie Filling
- 4 Medium Apples (Fuji, Honeycrisp, Gala, Granny Smith apples), peeled, cored, and diced
- 60 grams Butter
- 100 grams Brown Sugar
- 2 tsp Cinnamon
- Pinch of Salt
- 1 Tbsp Flour or Cornstarch
Instructions
- Preheat your oven to 400°F and line muffin pan(s) with liners or grease.
- In the large bowl, whisk together melted butter, sourdough, sour cream, egg, vanilla, and sugar until smooth.
- Mill your wheat into the wet ingredients and then add baking powder, baking soda, salt, and cinnamon.
- Gently fold the flour mixture and wet ingredients together. Then slowly fold in the apple pie filling.
- Fill cupcake liners about 2/3 full of batter and let rest on the counter for 5-10 minutes.
- Bake for about 15 minutes, or until internal temp is 200°F. Let cupcakes rest in the pan 5 minutes, then transfer to a wire rack to cool fully.
- While cupcakes are baking, make the frosting. Melt and whisk brown sugar and milk in a saucepan over medium heat for 3-5 minutes, remove from heat, add vanilla and salt, then let it cool.
- In a small mixing bowl, beat softened cream cheese and butter, and cinnamon until smooth. Slowly add the cooled, melted sugar mixture while using a hand mixer to beat until a fluffy consistency is reached. Cover and place in fridge for 30-60 minutes.
- Once cupcakes are fully cooled, frost with a piping bag if desired, or spread on with a knife. Optionally, top with a dusting of cinnamon or a tiny dice of fresh apple.
For Apple Pie Filling:
- Peel, core, and dice apples.
- Melt butter in a saucepan over medium heat. Add in diced apples and cook for a few minutes.
- Add in brown sugar, cinnamon, and salt. Continue to cook for another 4-5 minutes, or until the sauce is shiny and apples have softened.
- Whisk in cornstarch or flour and cook for 3-5 minutes, or until thick.
Notes
- This recipe usually makes 18 cupcakes (when the batter is filled about 2/3 full)
- This batter texture will be similar to muffin batter and/or cake batter
- If you like more frosting coverage on your cupcakes, you may want to double the frosting recipe
- You can make the frosting the day before and keep it in the fridge until ready to frost, just re-whip before piping
- We make and can our own homemade apple pie filling each fall when the apple harvest comes in. If you don't have any on hand, you can make some using the recipe provided.
Nutrition Information
Yield 18 Serving Size 1Amount Per Serving Calories 332Total Fat 15gSaturated Fat 9gTrans Fat 1gUnsaturated Fat 5gCholesterol 51mgSodium 282mgCarbohydrates 47gFiber 3gSugar 31gProtein 4g
*This has not been evaluated by the FDA. Nutrition Label may not be accurate. This label has been automatically pulled, and ingredients may not be categorized correctly.
FAQs
Not usually. The tang is subtle and enhances the flavor but doesn’t overpower it.
No, you’ll still rely on baking powder and baking soda for lift. The discard adds texture, flavor, and moisture, not leavening strength.
You can bake a day ahead and store airtight in the fridge. Frost and assemble close to serving time.
In an airtight container in the fridge for 2-3 days. Let them come to room temperature before serving.
These cupcakes are incredible!!
I love sourdough so I’ll have to try these!