Sourdough Fall Muffins are a warm, cozy treat filled with the flavors of the season. With the gentle tang of sourdough combined with spices like cinnamon and nutmeg, these muffins have a perfect balance of sweet and a hint of zest. You’ll notice bits of apple or pumpkin adding moisture and that classic fall feel in every bite.
I love using leftover sourdough starter for these muffins because it adds such a nice depth of flavor, and it’s a great way to reduce waste in the kitchen. Plus, the spices and fall fruits make my whole kitchen smell amazing while they bake, which always feels so comforting on a crisp autumn morning. I usually stir in some chopped nuts or a sprinkle of oats on top for a little extra texture.
These muffins are great for breakfast alongside a hot cup of tea or coffee, or even as a wholesome snack during the day. I like wrapping them up for a little fall-themed picnic or packing them in lunchboxes for a sweet surprise. They have that just-right mix of cozy and fresh that makes you want to reach for another one before you’re even done with the first.
Key Ingredients & Substitutions
Sourdough Starter: This adds a subtle tang and keeps muffins moist. If you don’t have a starter, plain yogurt is a good substitute.
Grated Apple or Pumpkin: Both give moisture and fall flavor. You can swap pumpkin for sweet potato or even mashed banana for a different twist.
Spices: Cinnamon and nutmeg are fall staples here. If you don’t have cloves, just leave them out or add a pinch of ginger instead.
Nuts: Walnuts or pecans add crunch and depth. If you’re nut-free, try sunflower seeds or chopped dried fruit.
Oil or Butter: Oil keeps muffins tender, while butter adds richness. Use whichever you prefer; melted coconut oil works well too.
How Do I Make a Perfect Streusel Topping?
The streusel adds texture and sweet crunch on top. Use cold butter and cut it into dry ingredients. This creates little lumps that bake into crisp bits.
- Mix brown sugar, nuts, and cinnamon in a bowl.
- Add cold, cubed butter.
- Use a fork or pastry cutter to blend until crumbly, with small clumps.
- Sprinkle this on muffin batter before baking for a crunchy top.
This simple step makes muffins look and taste extra special every time.

Equipment You’ll Need
- Mixing bowls – I use a couple of bowls to separate the dry and wet ingredients easily.
- Whisk or spoon – helps to mix ingredients smoothly without lumps.
- Muffin tin – makes shaping the muffins easy and uniform.
- Paper liners or baking spray – ensures the muffins come out without sticking.
- Pastry cutter or fork – for making the streusel topping look crumbly and perfect.
- Wire rack – for cooling the muffins so they set properly.
Flavor Variations & Add-Ins
- Swap walnuts or pecans for chopped almonds or sprinkles of crystallized ginger for extra spice and crunch.
- Add dried cranberries or raisins into the batter for a sweet burst in every bite.
- Try using pureed butternut squash instead of pumpkin for a different fall flavor.
- Reduced sugar or alternative sweeteners can be used if you prefer less sweetness or want a dairy-free option.
How to Make Sourdough Fall Muffins
Ingredients You’ll Need:
Main Ingredients:
- 1 cup active sourdough starter (unfed or fed)
- 2 cups all-purpose flour
- 1 teaspoon baking soda
- ½ teaspoon baking powder
- 1½ teaspoons ground cinnamon
- ½ teaspoon ground nutmeg
- ¼ teaspoon ground cloves (optional)
- ½ teaspoon salt
- ½ cup granulated sugar
- ¼ cup brown sugar, packed
- 2 large eggs
- ½ cup vegetable oil or melted butter
- 1 teaspoon vanilla extract
- 1 cup grated apple or pureed pumpkin
- ½ cup chopped walnuts or pecans
- ¼ cup milk (if needed for consistency)
For the Streusel Topping:
- ¼ cup chopped walnuts or pecans
- ¼ cup brown sugar
- 1 teaspoon cinnamon
- 2 tablespoons cold butter, cubed
For the Glaze:
- ½ cup powdered sugar
- 1-2 tablespoons milk or cream
- ¼ teaspoon vanilla extract
How Much Time Will You Need?
This recipe takes about 15 minutes to prepare and 20-25 minutes to bake. Allow extra time for cooling and glazing your muffins before enjoying.
Step-by-Step Instructions:
1. Get Ready:
Preheat your oven to 350°F (175°C). Line a muffin tin with paper liners or grease it well to keep muffins from sticking.
2. Mix Dry Ingredients:
In a medium bowl, whisk together the flour, baking soda, baking powder, cinnamon, nutmeg, cloves (if using), and salt.
3. Mix Wet Ingredients:
In a large bowl, beat the eggs with the sourdough starter, granulated sugar, brown sugar, oil or melted butter, and vanilla extract until smooth.
4. Combine Apple or Pumpkin:
Stir in the grated apple or pureed pumpkin to add moisture and delicious fall flavor.
5. Mix Dry and Wet Ingredients:
Gradually fold the dry ingredients into the wet mixture gently, just until combined. If the batter feels too thick, add milk a tablespoon at a time until it’s thick but easy to scoop.
6. Add Nuts:
Fold in the chopped walnuts or pecans evenly into the batter.
7. Make the Streusel Topping:
In a small bowl, combine the chopped nuts, brown sugar, and cinnamon. Cut in the cold butter with a fork or pastry cutter until the mix looks like coarse crumbs with small lumps.
8. Fill Muffin Cups and Add Topping:
Spoon the muffin batter evenly into the prepared muffin cups, filling each about ¾ full. Sprinkle the streusel topping generously on each muffin.
9. Bake:
Bake for 20-25 minutes, or until a toothpick inserted into the center comes out clean and the muffins are lightly golden on top.
10. Prepare the Glaze:
While the muffins cool, whisk together powdered sugar, milk, and vanilla extract until smooth and pourable.
11. Glaze and Serve:
Drizzle the glaze over the warm muffins. Let them cool just a bit before serving so the glaze sets. Enjoy warm or at room temperature!
These sourdough fall muffins have a tender crumb with a slight tang, delicious fall spices, and a crunchy nutty topping. The sweet glaze adds the perfect finishing touch, making them a cozy treat for chilly days!
Can I Use Frozen Sourdough Starter for These Muffins?
Yes! Just thaw your frozen starter in the fridge overnight and bring it to room temperature before using. Give it a good stir to make sure it’s well combined before adding to the batter.
Can I Substitute the Apple or Pumpkin?
Absolutely! You can swap in grated pear, mashed banana, or pureed butternut squash for a similar moisture and fall flavor. Just make sure it’s not too watery to avoid thinning the batter too much.
How Should I Store Leftover Muffins?
Store leftover muffins in an airtight container at room temperature for up to 2 days. For longer storage, keep them in the fridge for up to a week or freeze them wrapped individually for up to 3 months.
Can I Make These Muffins Dairy-Free?
Yes! Use a dairy-free oil like coconut or vegetable oil, and substitute the milk in the glaze with any plant-based milk. The muffins will still be moist and tasty.
