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Sourdough Discard Apple Cinnamon Muffins Recipe

Published: May 22, 2025 · Modified: May 22, 2025 by Stephanie · This post may contain affiliate links · Leave a Comment

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As apple picking season is in full swing, there's nothing quite like the warm, cinnamon-kissed aroma of homemade muffins filling your kitchen. This delicious recipe for sourdough discard apple cinnamon muffins brings together tart, orchard-fresh apples, warm spices, and the subtle tang of sourdough starter, turning leftover discard into a fall treat that tastes like a sourdough apple pie in muffin form. Each bite is bursting with autumn flavor, from tender apple pieces to cinnamon and a hint of nutmeg.

Zoomed-in shot of a perfectly baked apple cinnamon muffin with a golden, crunchy streusel topping, ideal for cozy fall mornings.

Making these muffins is an irresistible way to celebrate the season. Whether you're looking to use up sourdough discard or just craving a comforting baked good on a crisp fall day, these muffins invite you to savor the cozy flavors of fall.

Zoomed-in shot of a perfectly baked apple cinnamon muffin with a golden, crunchy streusel topping, ideal for cozy fall mornings.

Table of Contents

  • Ingredients for the Apple Cinnamon Sourdough Muffins
  • Sourdough Apple Cinnamon Muffins Recipe
  • Tips for the Sourdough Apple Muffins
  • More Sourdough Discard Recipes

This post contains affiliate links, which means I make a small commission at no extra cost to you. See my full disclosure here.

Zoomed-in shot of a perfectly baked apple cinnamon muffin with a golden, crunchy streusel topping, ideal for cozy fall mornings.

Fall is one of our favorite times of year around here, the crisp air, the changing leaves, and all the cozy flavors that come with it. These apple cinnamon sourdough muffins are a staple in our kitchen once the weather starts to turn. We enjoy them so much! They’re soft, warmly spiced, and just sweet enough. And the smell! When they’re baking, the whole house fills with the most comforting aroma of apples and cinnamon. It instantly sets the tone for the season and makes everything feel a little more peaceful, a little more homey.

Overhead shot of labeled ingredients for sourdough discard apple cinnamon muffins including flour, brown sugar, cinnamon, nutmeg, apples, and sourdough starter discard on a marble countertop.

Ingredients for the Apple Cinnamon Sourdough Muffins

Dry Ingredients

  • 2 cups (240g)  all-purpose flour (or fresh milled wheat)
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • ½ teaspoon salt
  • 1 ½ teaspoons cinnamon
  • ½ teaspoon nutmeg

Wet Ingredients

  • 1 cup (100g) sourdough starter discard or active sourdough starter
  • ¾ (150g) cup light or dark brown sugar to be mixed with wet ingredients
  • ½ cup melted unsalted butter 
  • 2 large eggs
  • 1 ¼ cups  milk
  • 1 teaspoon vanilla extract

Add-Ins

  • 1 ¼ cups finely chopped crisp apples (peeled or unpeeled)

Crumble Topping:

  • ½ cup all-purpose flour
  • ½ cup brown sugar (packed)
  • ½ teaspoon ground cinnamon
  • ¼ teaspoon salt
  • ¼ cup cold unsalted butter (cubed)

Sourdough Apple Cinnamon Muffins Recipe

Mixing bowl with flour, cinnamon, nutmeg, baking powder, baking soda, and salt for making homemade sourdough discard muffins.

STEP 1: Preheat oven to 350°F. Line or grease a 12-cup muffin tin. In a large bowl, whisk together flour, baking soda, baking powder, salt, cinnamon, and nutmeg.

Glass bowl filled with eggs, sourdough discard, brown sugar, vanilla, and melted butter ready to be mixed for apple cinnamon muffins.

STEP 2: In a separate bowl, combine discard, melted butter, brown sugar, eggs, vanilla, and milk. Mix until smooth.

Mixing sourdough discard batter with wooden spoon in a large bowl, ready to add chopped apples for muffins.

STEP 3: Add the wet mixture to the dry ingredients and stir just until combined — don’t overmix.

Final muffin batter with visible apple pieces mixed and ready to scoop into a muffin tin for baking.

STEP 4: Gently fold in chopped apples.

Raw muffin batter with apple chunks portioned into a red silicone muffin pan, placed on a baking sheet.

STEP 5: Fill the muffin pan ¾ of the way up with muffin batter.

Hand sprinkling brown sugar cinnamon crumble over muffin batter for homemade sourdough discard apple muffins.

STEP 6: Next make the crumb topping by combining flour, brown sugar, cinnamon, and salt. Add the cold butter and cut it into the dry ingredients with a pastry cutter or fork until the mixture becomes crumbly. Sprinkle the crumble on top of the muffin dough.

Freshly baked sourdough discard muffins with streusel topping cooling in red silicone muffin pan.

STEP 7: Bake for 20–25 minutes, or until a toothpick comes out clean.

Close-up of baked apple cinnamon muffins with golden brown crumble topping on a baking tray.

STEP 8: Let cool in the pan for 5 minutes, then transfer to a rack to cool completely.


Tips for the Sourdough Apple Muffins

  • These freeze well! You can wrap individually for an easy grab-and-go breakfast or I just simply place them in a gallon sized freezer safe Ziploc baggie once they've cooled.
  • Try mixing in chopped pecans, shredded coconut, or raisins (one of our favorite add-ins!)for variation.
  • This recipe works great with tart apples like Granny Smith or Honeycrisp.

More Sourdough Discard Recipes

Just baked Milled Wheat Lemon Poppy Seed Sourdough Muffins.

Milled Wheat Lemon Poppy Seed Sourdough Muffins

Close-up of a golden-brown sourdough apple fritter with a glossy glaze, showing crispy edges and bits of apple for a cozy breakfast or dessert.

The Best Sourdough Discard Apple Fritters Recipe

Just baked sourdough brownies for Best Easy Fudgy Sourdough Brownies Discard Recipe.

Best Easy Fudgy Sourdough Brownies Discard Recipe

Just baked cinnamon rolls for Quick Sourdough Discard Cinnamon Rolls Easy Recipe

Quick Sourdough Discard Cinnamon Rolls Easy Recipe

Zoomed-in shot of a perfectly baked apple cinnamon muffin with a golden, crunchy streusel topping, ideal for cozy fall mornings.

Apple Cinnamon Sourdough Discard Muffins Recipe

This delicious recipe for Apple Cinnamon Sourdough Discard Muffins brings together tart, orchard-fresh apples, warm spices, and the subtle tang of sourdough starter, turning leftover discard into a fall treat that tastes like a sourdough apple pie in muffin form.
Print Pin Rate
Course: Appetizer, Breakfast, Side Dish, Snack
Cuisine: American
Keyword: apple, bowl, muffin, muffins, Sourdough
Prep Time: 10 minutes minutes
Cook Time: 20 minutes minutes
Total Time: 30 minutes minutes
Servings: 0
Author: Stephanie

Ingredients

Dry Ingredients

  • 2 cups (240g) all-purpose flour or fresh milled wheat
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • ½ teaspoon salt
  • 1 ½ teaspoons cinnamon
  • ½ teaspoon nutmeg

Wet Ingredients

  • 1 cup sourdough starter discard or active sourdough starter
  • ¾ cup (150g) light or dark brown sugar to be mixed with wet ingredients
  • ½ cup melted unsalted butter
  • 2 large eggs
  • 1 ¼ cups milk
  • 1 teaspoon vanilla extract

Add-Ins

  • 1 ¼ cups finely chopped crisp apples peeled or unpeeled

Crumble Topping:

  • ½ cup all-purpose flour
  • ½ cup brown sugar packed
  • ½ teaspoon ground cinnamon
  • ¼ teaspoon salt
  • ¼ cup cold unsalted butter cubed

Instructions

  • Preheat oven to 350°F. Line or grease a 12-cup muffin tin.
  • In a large bowl, whisk together flour, baking soda, baking powder, salt, cinnamon, and nutmeg.
  • In a separate bowl, combine discard, melted butter, brown sugar, eggs, vanilla, and milk. Mix until smooth.
  • Add the wet mixture to the dry ingredients and stir just until combined — don’t overmix.
  • Gently fold in chopped apples.
  • Fill the muffin pan ¾ of the way up with muffin batter.
  • Next make the crumb topping by combining flour, brown sugar, cinnamon, and salt. Add the cold butter and cut it into the dry ingredients with a pastry cutter or fork until the mixture becomes crumbly. Sprinkle the crumble on top of the muffin dough.
  • Bake for 20–25 minutes, or until a toothpick comes out clean.
  • Let cool in the pan for 5 minutes, then transfer to a rack to cool completely.

Notes

  • These freeze well! You can wrap individually for an easy grab-and-go breakfast or I just simply place them in a gallon sized freezer safe Ziploc baggie once they've cooled.
  • Try mixing in chopped pecans, shredded coconut, or raisins (one of our favorite add-ins!)for variation.
  • This recipe works great with tart apples like Granny Smith or Honeycrisp.

More Breakfast Ideas

  • Freshly whipped cinnamon honey butter piped into small serving bowls with slices of sourdough bread.
    Homemade Whipped Honey Butter Recipe 
  • Plate of thin, golden sourdough crepes stacked with fresh strawberries and a swirl of strawberry whipped cream, served with a fork.
    Easy Sourdough Discard Crepes Recipe
  • Spoonful of creamy homemade yogurt being lifted from a green ceramic bowl, surrounded by fresh strawberries and granola—perfect for a nutritious breakfast or snack.
    How to Make Homemade Yogurt Without a Yogurt Maker 
  • White baking dish filled with colorful cherry tomatoes, whole garlic cloves, and fresh thyme sprigs submerged in olive oil, prepared for oven-roasted tomato confit with garlic and herbs.
    Cherry Tomato Confit Recipe with Garlic and Thyme

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