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sourdough pumpkin muffin inside with chocolate chips peaking through sitting on blue and white china

Sourdough Pumpkin Muffins

Kyrie | Healthfully Rooted Home
These sourdough pumpkin muffins are so perfectly flavored and textured and they use all clean ingredients.
Prep Time 15 mins
Cook Time 20 mins
Total Time 35 mins
Course Breakfast, Dessert, Snack
Cuisine American
Servings 27 muffins
Calories 135 kcal


  • Large bowl
  • Muffin tin
  • Spatula
  • whisk


  • 3/4 cup coconut oil
  • 3 large eggs
  • 2 tsp vanilla extract
  • 2 cups coconut sugar
  • 30 oz pumpkin puree pure, organic
  • 1 cup sourdough starter discard or active
  • 2 1/2 cups flour
  • 1 tsp sea salt
  • 1 tsp baking soda
  • 1 tsp baking powder
  • 2 tbs pumpkin pie spice
  • 1 cup chocolate chips

Cinnamon Sugar Topping

  • 1/4 cup coconut sugar
  • 1 tbs pumpkin pie spice


  • Preheat your oven to 375 degrees F.
  • In a large bowl, whisk the oil, eggs, vanilla, sugar and pumpkin.
  • Use a spatula to fold in your sourdough starter.
  • Add the flour, salt, baking powder, baking soda and pumpkin pie spice. Mix until just combined (don't overmix).
  • Gently fold in the chocolate chips.
  • Grease a muffin tin with coconut oil.
  • Pour the batter into the muffin tin filling about 3/4 full.
  • Mix the sugar and pumpkin spice in a small bowl.
  • Sprinkle the pumpkin spice sugar over the sourdough pumpkin muffin batter.
  • Bake for about 20 mins or until a toothpick inserted into the center of the muffins comes out clean.
  • Cool for about 5 minutes until the muffins loosen from the muffin tin and then rest on a cooling rack.
  • Store in an airtight container at room temperature for about 3 days or freeze for up to 3 months.



  • Your sourdough starter doesn't have to be active and bubbly. I make this recipe using my sourdough discard right after pulling it out of the fridge.
  • If you don't have a sourdough starter yet, you can substitute the starter for buttermilk.
  • Don't overmix the sourdough muffin batter. to prevent overmixing, start by mixing the wet ingredients, then gently fold in the dry ingredients.
  • Use paper liners only if you aren't planning on eating the muffins right away. If you're planning on eating the muffins within 1-2 days, simply grease the muffin tin.
  • Use an ice cream scoop to scoop the batter into the muffin tin.
  • Don't overfill your muffin tins. 3/4 full is the optimal amount of batter in order to get nicely domed muffin tops.
  • Remove your muffins from the muffin tin after about 5 minutes. This will ensure that they won't crumble, but they won't cook too long either.
  • Don't use pump pie filling. Pumpkin pie filling is not the same thing as pumpkin puree. This recipe calls for pure pumpkin puree made from organic pumpkins. You don't want all the added sugar and spices from pumpkin pie filling to overpower the ingredients I call for.
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