Experience the best pumpkin muffins that are soft, moist, and topped with a tangy cream cheese filling. These muffins are simple to make, perfect for holiday gatherings, and sure to become a family favorite!
Table of Contents

The Best Pumpkin Muffins with Cream Cheese Filling
Why You’ll Love These Pumpkin Muffins
These pumpkin muffins are a delightful treat with their fluffy texture and warm, spiced flavor. The addition of cream cheese filling adds a creamy, indulgent twist, making them perfect for any occasion. They’re also family-friendly and great for meal prep, allowing you to whip up a batch quickly and enjoy them throughout the week.
Ingredients for Pumpkin Muffins
- 120 g All-purpose Flour (1 cup)
- 1 tsp Baking Powder
- 1 tsp Baking Soda
- ½ tsp Kosher Salt
- 2 tsp Pumpkin Pie Spice (or 1 tsp ground cinnamon and ¼ tsp each of ground nutmeg, ginger, cloves, and allspice)
- 337 g Pumpkin Puree (1 ½ cups)
- 104 g Light Brown Sugar (½ cup)
- 50 g Granulated Sugar (¼ cup)
- 2 Eggs
- 120 g Sourdough Discard (½ cup) or active sourdough starter
- 1 tsp Vanilla Extract
- 113 g Unsalted Butter, melted (½ cup or 1 stick)
- 113 g Cream Cheese, softened (4 oz)
- 2 TBS Granulated Sugar (for filling)
- Pumpkin Seeds/Pepitas (for topping)
Ingredients for Cream Cheese Filling
- 113 g Cream Cheese, softened (4 oz)
- 2 TBS Granulated Sugar
How to Make Pumpkin Muffins with Sourdough Discard
Preheat Oven and Prepare Muffin Tin
Start by preheating your oven to 350ºF (177ºC). Line a muffin pan with liners and spray them lightly with non-stick baking spray to ensure easy removal later.
Mix Dry Ingredients
In a small bowl, whisk together the flour, baking powder, baking soda, kosher salt, and pumpkin pie spice. Set this mixture aside while you prepare the wet ingredients.
Combine Wet Ingredients for Muffin Batter
In a large bowl, combine the pumpkin puree, light brown sugar, granulated sugar, eggs, sourdough discard, and vanilla extract. Whisk these ingredients together until well combined and shiny. Add the melted butter last, mixing until fully incorporated.
Create the Cream Cheese Filling
In a separate bowl, whisk the softened cream cheese and 2 tablespoons of sugar until light and airy. Be careful not to over-whip; you want a smooth consistency that will blend perfectly into your muffins.
Assemble the Pumpkin Muffins

Now, spoon the muffin batter into the prepared liners, filling them about three-quarters full. Next, add approximately one tablespoon of the cream cheese filling on top of each muffin. For a fun twist, you can also pipe the filling into the center of the muffin batter before topping with more batter.
Bake and Cool the Muffins
Bake the muffins in your preheated oven for 17-20 minutes or until a toothpick inserted into the center comes out clean. Once done, let them cool on a wire rack. The aroma of pumpkin and spice will fill your kitchen, inviting everyone to join you for a treat!
Tips for Perfect Pumpkin Muffins
Sourdough Discard vs. Active Starter
If you have sourdough discard, feel free to use it in this recipe. An active sourdough starter can also work beautifully, adding a slightly different flavor profile.
Achieving the Right Cream Cheese Consistency
Be sure to whisk the cream cheese filling until it’s light but not overly whipped. This ensures a smooth filling that will complement the muffins perfectly.
Baking Time and Doneness Test
A toothpick test is your best friend here. If it comes out clean, your muffins are done! Adjust the baking time slightly if your oven runs hot or cold.
FAQs
What ingredients do I need for best pumpkin muffins?
You need all-purpose flour, baking powder, baking soda, kosher salt, pumpkin pie spice, pumpkin puree, light brown sugar, granulated sugar, eggs, sourdough discard or active starter, vanilla extract, melted unsalted butter, softened cream cheese, and pumpkin seeds for topping.
How do I make best pumpkin muffins step by step?
Start by preheating the oven and preparing your muffin tin. Then, mix the dry ingredients, combine the wet ingredients, make the cream cheese filling, assemble the muffins, and bake until golden brown.
Can I make best pumpkin muffins ahead of time?
Absolutely! You can prepare the batter and fill the muffin tins ahead of time. Just store them in the refrigerator and bake when you’re ready to enjoy.
How should I store leftover best pumpkin muffins?
Store the leftover muffins in an airtight container at room temperature for up to three days, or refrigerate them for longer freshness.
Related Recipes to try
- Pumpkin Zucchini Bread Recipe Delicious And
- Zucchini Carrot Muffins
- Apple Cinnamon Zucchini Muffins
- Double Chocolate Zucchini Muffins
- Zucchini Muffin Recipe For Baby
- Zucchini Muffin Recipe For Baby 2
Conclusion
You can enjoy these scrumptious best pumpkin muffins as a delightful treat during the festive season. They’re quick to whip up and perfect with a warm cup of coffee. For more inspiration, you can check out Pinterest for countless ideas and recipes to bring joy to your kitchen.

The Best Pumpkin Muffins with Cream Cheese Filling – Irresistibly Delicious!
Equipment
- skillet
- mixing bowl
- whisk
Ingredients
- 120 g All-purpose Flour 1 cup
- 1 tsp Baking Powder
- 1 tsp Baking Soda
- ½ tsp Kosher Salt
- 2 tsp Pumpkin Pie Spice or 1 tsp ground cinnamon and ¼ tsp each of ground nutmeg, ginger, cloves, and allspice
- 337 g Pumpkin Puree 1 ½ cups
- 104 g Light Brown Sugar ½ cup
- 50 g Granulated Sugar ¼ cup
- 2 Eggs
- 120 g Sourdough Discard (½ cup) or active sourdough starter
- 1 tsp Vanilla Extract
- 113 g Unsalted Butter, melted ½ cup or 1 stick
- 113 g Cream Cheese, softened 4 oz
- 2 TBS Granulated Sugar for filling
- Pumpkin Seeds/Pepitas for topping
Instructions
- Preheat oven to 350ºF (177ºC). Line muffin pan with liners and spray with non-stick baking spray.
- Whisk dry ingredients (flour, baking powder, baking soda, salt, spice) in a small bowl and set aside.
- In a large bowl, whisk wet ingredients (pumpkin puree, sugars, eggs, sourdough discard, vanilla). Add melted butter last and whisk until fully incorporated and shiny.
- Pour dry ingredients into wet mixture and whisk just until combined.
- Whisk softened cream cheese and 2 TBS sugar in a separate bowl until light and airy, but not over-whipped.
- Spoon batter into prepared muffin liners about ¾ full.
- Add approximately 1 tablespoon of cream cheese filling on top of each muffin (alternatively, pipe into the center and top).
- Sprinkle tops with pumpkin seeds.
- Bake for 17-20 minutes until a toothpick inserted into the center comes out clean.
- Cool on a wire rack.
Notes
– Active sourdough starter can be substituted for sourdough discard.
– Cream cheese filling should be whisked until light but not totally whipped.
– Filling can be applied by spooning on top or piping into the center and top.




