Sourdough Pumpkin Cream Cheese Muffins (Easy and Delicious)

Name: Sourdough Pumpkin Cream Cheese Muffins
Prep time: 30 min
Cook time: 15 min
Total time: 45 min
Ingredients: 310 grams all-purpose flour (2 cups + 1/4 cup); 8 grams baking powder (2 teaspoons); 10 grams baking soda (1 1/2 teaspoons); 5 grams ground cinnamon (2 1/2 teaspoons); 4 grams pumpkin pie spice (2 teaspoons); 6 grams salt (1 teaspoon); 120 grams sourdough discard, room temperature (1/2 cup); 100 grams granulated sugar (1/2 cup); 110 grams light brown sugar (1/2 cup); 150 grams eggs, room temperature (about 3 large eggs); 425 grams pure pumpkin puree, canned (15 ounces); 113 grams unsalted butter, melted (1/2 cup ); 226 grams full-fat block cream cheese, softened (8 ounces); 40 grams white sugar (about 3 Tablespoons + 1 teaspoon); 4 grams vanilla extract or vanilla bean paste (1 teaspoon); 5 grams all-purpose flour (1 1/2 teaspoons); pinch of salt; 60 grams all-purpose flour (1/4 cup + 2 Tablespoons); 50 grams light brown sugar (1/4 cup); .5 gram pumpkin pie spice (1/4 teaspoon); 42 grams unsalted butter, melted (3 Tablespoons)

These Sourdough Pumpkin Cream Cheese Muffins are soft, warmly spiced, and filled with a rich cream cheese center, then finished with a buttery crumble topping. They were inspired by the Starbucks favorite, but I love being able to make them at home with sourdough and simple ingredients whenever that first pumpkin craving hits!

I adapted them from my Sourdough Pumpkin Chocolate Chip Muffins, which are another easy fall favorite. For even more cozy pumpkin recipes, try my Sourdough Pumpkin Quick Bread or these crisp Sourdough Pumpkin Waffles next!

Table of Contents

Quick Look: Sourdough Pumpkin Cream Cheese Muffins

Prep Time: 30 minutes
Cook Time: 15 minutes
Total Time: 45 minutes
Servings: 15 muffins
Calories: ~ 328kcal per muffin (based on nutritional panel)
Cook Method: Baked
Flavor Profile: Moist, warmly spiced pumpkin muffins with a luscious cream cheese center and a crunchy crumble topping. A homemade upgrade on the Starbucks classic!
Difficulty: Easy to Intermediate — A few components to prep, including the cream cheese filling and crumble topping, but each step is simple and quick!

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Why You’ll Love Sourdough Pumpkin Cream Cheese Muffins

Make them now or prep them the night before — If you want muffins today, you can mix the batter and bake them right away. Or, if you prefer a long fermentation, let the batter rest in the fridge overnight and bake them fresh the next morning. My Sourdough Pumpkin Chocolate Chip Muffins give you that same flexibility.
You’ll use the whole can of pumpkin — No leftover pumpkin puree sitting in the fridge! This recipe uses the entire can, which is always a win in my book.
Soft, creamy, and crunchy all in one — The muffins bake up soft and moist, with a creamy center and a buttery crumble topping for the perfect mix of textures. If you love a good muffin top, my Sourdough Apple Cinnamon Muffins are another favorite.
There’s cream cheese in every bite — The cream cheese filling sits right in the center of each muffin, so you get a little with every bite instead of just a dollop on top. For another cozy pumpkin bake, try my Sourdough Pumpkin Coffee Cake next.

Ingredients & Substitutions

* To find precise measurements, scroll to the bottom of this post to find the recipe card*

ingredients for making sourdough pumpkin cream cheese muffins

Flour—I used all-purpose flour for this recipe.
Sugar—I used both white and light brown sugar for a subtle caramel flavor, but you can use only white sugar.
Eggs—Use room-temperature eggs so the ingredients mix properly and the batter rises to that perfect dome shape.
Sourdough Starter Discard—I prefer using fresh sourdough discard, about 1–2 days old, for sweet treats like this. If you don’t have discard on hand, you can use an equal amount of active sourdough starter, measured in grams.
Unsalted Butter—Reduce the salt by 1 gram (1/4 tsp) if you use salted butter.
Spices—A combination of ground cinnamon and pumpkin pie spice brings the perfect warmth to these muffins. If you don’t have pumpkin pie spice, you can easily make your own at home.
Pumpkin Puree—I used an entire can of pumpkin purée, NOT pumpkin pie filling. I haven’t tested this recipe with homemade pumpkin puree, but if you try it, please let me know how it goes.
Vanilla Extract—It goes into both the muffin batter and the cream cheese filling for a warm, rounded flavor.

Cream Cheese Filling

Cream Cheese— I used full-fat cream cheese to whip up this sweet cream cheese filling. Let it come to room temperature for easier mixing.
Flour—A touch of flour helps to thicken the filling while the muffins bake.
Vanilla Extract—I used vanilla bean paste, but you can opt for vanilla extract as well! I just love the little specks that vanilla bean paste adds to the cream cheese filling.

How to Make Sourdough Pumpkin Cream Cheese Muffins

Preheat the oven to 425°F and line a muffin tin with muffin liners. Set aside.

In a large bowl, whisk together the dry ingredients. Set to the side.

In a medium bowl, add the wet ingredients and whisk until combined and smooth.

Add the wet ingredients to the dry ingredients and mix until just combined. Let the batter rest for 15 minutes.

In a small bowl, add the cream cheese filling ingredients and beat until smooth. Place the cream cheese mixture to a piping bag and set aside.

crumble topping for sourdough cream cheese muffins

In another small bowl, add the crumble topping ingredients and mix until crumbly. Set aside.

sourdough pumpkin cream cheese muffin batter into the muffin tin

After resting, scoop the muffin batter into the muffin tin until about 90% full.

Insert the piping bag into the batter until you touch the bottom, then slowly squeeze in the cream cheese filling.

sprinkled crumble topping into the muffin batter

Finally, sprinkle the crumble over each muffin, working around the cream cheese filling.

Bake at 425°F for 7 minutes, then at 350°F for 8-10 minutes more.

baked sourdough pumpkin cream cheese muffins

Leave the muffins in the muffin tin for 5 minutes before placing them on a wire rack to cool completely. Enjoy!

McKenna’s Helpful Tips

Don’t overmix the pumpkin muffin batter. Mix just until the dry ingredients disappear. Overmixing makes the muffins dense, and who wants that? My Sourdough Pumpkin Scones call for the same light hand.
Room-temperature eggs work best. Room-temperature eggs work best. The batter mixes evenly, and the muffins get the nice rounded tops we all love. Ingredient temperature matters just as much in my Sourdough Pumpkin Dutch Baby.
Poke the toothpick in the muffin, not the filling. The sweet cream cheese center stays soft even when the muffin is done, so it’ll coat the toothpick. Bake until the toothpick comes out clean from the muffin itself.
Don’t skip the 15-minute rest. It gives the flour time to hydrate, which makes the muffins extra fluffy. Use that time to make the cream cheese filling and the crumble topping.
Overnight option: Prepare the muffin batter the night before, leaving out a few of the ingredients, cover, and chill in the fridge overnight. The following morning, whisk in the eggs, melted butter, ground cinnamon, pumpkin spice, and vanilla extract. Bake as usual. I do the same exact thing for my Sourdough Blueberry Muffins!

How to Store

These have a cream cheese filling, so leftover sourdough pumpkin muffins belong in the fridge once they’ve cooled. They shouldn’t sit out for more than 2 hours. Store them in an airtight container for 3 to 4 days. If you’d like to freeze them, wrap each cooled muffin in plastic wrap, tuck the wrapped muffins into a freezer-safe bag, and freeze for up to 3 months. Thaw them overnight in the fridge, then reheat in a 350°F oven for 5-10 minutes to bring back the crunch of the crumble topping. You can also microwave them for 15-20 seconds.

broken in half muffins showing cream cheese

Sourdough Pumpkin Cream Cheese Muffins FAQs

Can I use an active starter for these sourdough pumpkin muffins?

Yes! Swap in the same amount of active starter, measured in grams. The starter mainly adds sourdough flavor, while the baking powder and baking soda handle the rise. For a 100% sourdough recipe that relies on a bubbly starter for the rise, you’ll like this Sourdough Pumpkin Bread.

Can I use homemade pumpkin puree for sourdough pumpkin muffins?

I haven’t tested this recipe with homemade pumpkin puree, so I can’t promise the same results. Homemade puree usually contains more water than canned, which can make the batter wetter than it should be. I had the same concern with my Sourdough Pumpkin Bagels, where I advised using less water if you choose to use homemade puree.

Why does the muffin batter need to rest for 15 minutes?

The short rest gives the flour time to hydrate, which helps make the muffins extra fluffy. It also gives you time to prepare the cream cheese filling and crumble topping before filling the muffin tin.

Sourdough Pumpkin Cream Cheese Muffins (Easy and Delicious)

Quick Look: Sourdough Pumpkin Cream Cheese Muffins

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Why You’ll Love Sourdough Pumpkin Cream Cheese Muffins

Ingredients & Substitutions

Cream Cheese Filling

How to Make Sourdough Pumpkin Cream Cheese Muffins

McKenna’s Helpful Tips

How to Store

Sourdough Pumpkin Cream Cheese Muffins FAQs

More Pumpkin Sourdough Recipes

Sourdough Pumpkin Waffles Recipe (With Active Starter)

Homemade Sourdough Pumpkin Pie (From Scratch)

Sourdough Pumpkin Scones Recipe with Maple Glaze

Sourdough Pumpkin Quick Bread Recipe