Sourdough Pumpkin Cream Cheese Muffins

Filled with real pumpkin puree, pumpkin pie spices, sourdough discard, and cream cheese, these Sourdough Pumpkin Cream Cheese Muffins are the perfect fall treat and probably my favorite muffin ever!

While PSLs (pumpkin spice lattes) get all of the love from Starbucks, they also make a seasonal pumpkin cream cheese muffin that inspired this copycat recipe.

You can use active sourdough starter or sourdough discard in this moist sourdough pumpkin muffin recipe. With the natural tang of sourdough and cream cheese, these muffins aren’t too sweet and the pumpkin spices do not overpower the pumpkin puree (which can be a problem for pumpkin-spiced desserts!).

Finally, they’re easy to make! They take about 30 minutes to bake up, so you don’t have any excuse for not baking these autumnal breakfast muffins.

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👍 Why You’ll Love This Recipe

• Made with real pumpkin:
  • Like making Sourdough Strawberries & Cream Scones, I like using real fruit or real puree to make these sourdough discard pumpkin muffins! Pumpkin is such a great baking ingredient because it adds a subtle earthy flavor, beautiful orange color, and natural moistness to baked goods.
• Crunchy topping:
  • Like my Buckwheat Sourdough with Pumpkin Seeds or Seeded Whole Wheat Sourdough Sandwich Bread, adding seeds to the top of baked goods gives a lovely crunch to an otherwise soft treat.
  • The textural contrast of a crunchy outside and soft center is one of the reasons why sourdough bread is so loved!
  • If you don’t have pumpkin seeds, or pepitas, you could use sunflower seeds, oats, or chopped pecans.
• Cream cheese centers:
  • Okay, so the cream cheese centers really take these sourdough pumpkin muffins from great to amazing! The cream cheese pairs so well with the pumpkin spice flavors by adding a slight tang and creaminess to the center of the muffins.
  • You can exclude it from the recipe, but the extra few minutes it takes to add it is worth it!
• It’s a Starbucks copycat recipe:
  • These pumpkin muffins are a copycat of these Pumpkin Cream Cheese Muffins from Starbucks. So, if you’re a fan of those muffins, you’re gonna adore these!
  • Making them from home is so easy and they have fewer ingredients and less added sugar than the Starbucks version (although, I will have you know that their muffins are made with actual pumpkin, which even surprised me).
• No oil:
  • I only use butter in this recipe as the fat and don’t use vegetable oil. Like my Sourdough Zucchini Bread and Sourdough Banana Bread recipes, I try to avoid using too much vegetable oil in recipes because it doesn’t add any flavor!
  • Instead, the melted butter adds richness, tenderness, and so much flavor to these muffins like in my Sourdough Chocolate Muffins.

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👨‍🍳 Tips for Making the Best Sourdough Pumpkin Muffins

• Don’t overmix the batter
  • Overmixing leads to gluten development, which will create a tough batter, just like making tender Sourdough Irish Soda Bread or these other Sourdough Bran Muffins. Like cake or pastry, you want to limit the mixing here so you get tender and soft muffins.
• Use pumpkin puree, not pumpkin pie filling
  • Like my Sourdough Pumpkin Waffles, only use real pumpkin puree in this recipe. Pumpkin pie filling includes sugar and spices, so using it will cause these muffins to be too sweet. I highly recommend using Libby’s 100% Pure Pumpkin!
• How to prevent sinking middles
  • Some sinking in the middle of these muffins is normal (even the Starbucks ones do it!). However, adding cream cheese to the middle of the muffins increases the chance of collapsing middles.
  • To prevent sinking middles, make sure to bake the muffins long enough until a toothpick comes out clean, don’t open the oven door during baking, and ensure that your leavening agents are still active.
• Use pumpkin pie spice or a mix of spices
  • You can use pre-mixed pumpkin pie spice or make your own mix of spices for this recipe. I include both in the recipe, so you can spice them to perfection! However, you’re welcome to add or exclude other warming spices to your liking.
• Grease the muffin liners
  • It’s best to grease or spray your muffin liners with non-stick spray before adding the batter. That way, the muffins won’t stick too as much to the liners once they cool.

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🛠 Tools Needed:

Click the links below for my tool recommendations.

• Baking Scale
  • Regarding sourdough starter, it’s important to note that standard measurements can differ greatly depending on the individual. Therefore, weighing will provide the most accurate results.
• 12-cup Muffin Pan
  • This recipe makes 12 standard-sized muffins. You’ll need a standard muffin or cupcake pan to make the recipe.
  • If you’re looking to make this recipe a bread loaf pan, check out my Sourdough Pumpkin Chocolate Chip Bread, which is almost the exact same batter!
• Muffin Liners
  • If you use a non-stick pan or you grease your pan really well, you technically don’t need muffin liners. However, the liners do prevent sticking, help you transport the muffins, and are a better way to serve the muffins to family or guests.
  • While I like tulip liners for my apple muffins, I prefer typical muffin liners for these muffins so you get clear muffin tops and can easily spoon the cream cheese and sprinkle the pumpkin seeds on top.
• Whisk
• Spatula, for scraping the sides of the bowl
• Cookie Scoop (or ice cream scoop), optional
  • A large cookie scoop is optional, but I really like using one to help get equal-sized muffins! Plus, it’s cleaner and more satisfying to me than pouring or spooning the batter into the pans.  Alternatively, a greased ¼ cup scoop works well too.

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🛒 Ingredients Needed:

Click on the links below for my favorite ingredient recommendations. Ingredient substitutions are also listed below.

Sourdough Pumpkin Muffins

• All-purpose Flour
  • There’s only a cup of flour in this recipe, not including the sourdough discard. All-purpose works best, but you’re welcome to substitute some of it with whole wheat flour if you’d like.
• Baking Powder
  • This muffin batter isn’t fermented, so the sourdough doesn’t add any leavening to the recipe. Thus, the baking powder and baking soda are the mechanical leaveners that both help the muffins rise tall and stay fluffy.
• Baking Soda
  • Both baking powder and soda go bad over time. Learn how to test yours here.
• Salt
• Pumpkin Pie Spice
  • Pumpkin pie spice, or pumpkin spice, is a pre-mixed spice of cinnamon, nutmeg, cloves, ginger, and allspice. If you have it, you can use it directly in this recipe! 
  • However, you can also use the individual spices if you don’t have pumpkin pie spice. To make your own pumpkin pie spice for this recipe, combine 1 tsp of cinnamon, and ¼ tsp each of ground nutmeg, cloves, ginger, and allspice.
• Pumpkin Puree
  • Pumpkin puree is 100% canned pumpkin, or squash. Libby’s 100% Pure Pumpkin is the best quality and very consistent. Don’t use pumpkin pie filling since it’s already sweetened and spiced.
  • If you buy a 15 oz can, this recipe leaves about ¼ cup of puree leftover (sorry!). I tried to use the whole can in recipe testing, but there was a little too much batter for 12 muffins!
  • If you want to go the extra mile, you can also roast your own pumpkin or squash and puree it to use in the recipe.
• Light Brown Sugar
  • Brown sugar provides sweetness and also adds more moisture and flavor from the added molasses. This complements the warming pumpkin spices.
• Granulated Sugar
• Eggs
• Sourdough Discard
  • If you don’t have an active sourdough starter, learn how to make one in a week following my how-to guide. See my top sourdough starter tips here.
• Vanilla Extract
• Unsalted Butter, melted
  • There’s no oil in this recipe. The melted butter adds richness and needed fat for moisture.
• Pumpkin Seeds, for topping (optional)
  • I use raw pumpkin seeds, or pepitas, to top the muffins for crunch and color. They toast slightly in the oven. You can also substitute with sunflower seeds or chopped pecans, or leave them out completely.

Cream Cheese Filling

• Cream Cheese, softened
  • Philadelphia Cream Cheese is my go-to brand for consistency and the best flavor. It’s silkier and has a lower moisture content than other brands, which works well for this recipe or for my Sourdough Cinnamon Rolls with Brown Butter Cream Cheese Frosting.
• Granulated Sugar

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🎃 How to Make Sourdough Pumpkin Cream Cheese Muffins

Follow this visual and detailed recipe guide as you make these sourdough pumpkin muffins.

1. Mix the Dry Ingredients

Preheat the oven to 350ºF (177ºC). Then, line your muffin pan with muffin or cupcake liners and give them a quick spray with non-stick baking spray.

Whisk the dry ingredients together in a small bowl, including:

• 120 grams of all-purpose flour (one cup)
• 1 teaspoon of baking powder
• 1 teaspoon of baking soda
• ½ teaspoon of salt
• 2 teaspoons of pumpkin pie spice
  • Alternatively, use 1 teaspoon of ground cinnamon and ¼ teaspoon each of ground nutmeg, cloves, ginger, and allspice.

Set aside.

2. Mix the Wet Ingredients

In a large mixing bowl, whisk together the following wet ingredients:

• 337 grams of pumpkin puree (1 ½ cups)
• 104 grams of light brown sugar (½ cup)
• 50 grams of granulated sugar (¼ cup)
• 2 eggs
• 120 grams of sourdough discard (½ cup)
• 1 teaspoon of vanilla extract

Then, pour in 113 grams of melted unsalted butter (½ cup, 1 stick).

Whisk in the melted butter until the mixture is bright orange and shiny.

3. Mix the Batter

Pour the dry ingredients to the bowl of wet ingredients and slowly mix until just combined.

To avoid overmixing, only mix until you can’t see any more white floury specks.

Then, set aside or refrigerate the batter while you make the cream cheese filling.

4. Make the Cream Cheese Filling

The cream cheese mixture is super easy to make! I often use a stand mixer here, but you could easily use a hand mixer or mix by hand since it’s such a small amount.

In a medium-sized bowl, whisk together 113 grams of softened cream cheese (4 oz) and 2 TBS of granulated sugar until the cream cheese is light and fluffy.

The mixture shouldn’t be quite as light as whipped cream cheese, so don’t take it that far. You’re just looking to incorporate the sugar and add some air to the cream cheese.

5. Add the Cream Cheese Filling

Transfer the sourdough discard pumpkin muffin batter to the prepared muffin pan and greased liners.

Fill the muffin cups ¾ of the way. There should be just enough batter for all twelve muffins!

I like to use a large cookie scoop (3-4 TBS) to get equal-sized proportions. But you can also use a spoon or spatula.

Then, add the cream cheese filling. You can opt to use a piping bag to pipe about a tablespoon of cream cheese filling into the center and tops of the muffins (this most resembles the Starbucks muffins) or spoon a tablespoon of cream cheese on top.

Both ways work well. I think piping looks neater and you’re able to get cream cheese more into the center of the muffins. However, I found that piping also increases the likelihood of the centers falling slightly during cooling.

For another effect, you can swirl the cream cheese on top with a toothpick for swirled pumpkin muffins!

Lastly, sprinkle raw pumpkin seeds on top of the muffins all around the cream cheese center.

6. Bake

Bake the muffins at 350ºF (177ºC) for 17-20 minutes, or until a toothpick inserted into the middle comes out clean.

Finally, cool on a wire rack before devouring!

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How to Store Sourdough Pumpkin Cream Cheese Muffins

Because of the cream cheese centers, the sourdough pumpkin muffins should be refrigerated if not eaten in a few hours.

I think they’re excellent slightly chilled as the cream cheese filling sets well. And this way, you can store them in the refrigerator for up to six or seven days. 

They’re best within the first few days, though.

Can I Freeze?

While most muffins freeze well, and you can freeze these, I don’t recommend it.

That’s because the cream cheese filling loses some of its flavor, color, and texture when frozen. It’s just not as pleasurable as an experience to eat these muffins thawed. 

However, if you leave out the cream cheese filling, you can freeze the baked muffins for up to a few months in a freezer-safe bag.

Then, you can spoon some room temperature cream cheese on top of them if you’d like or serve on the side!

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Sourdough Pumpkin Cream Cheese Muffins FAQs:

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