Welcome to the ultimate autumn baking experience! Prepare to fall in love with these extraordinary Pumpkin Cream Cheese Muffins. Far beyond your average baked good, these aren’t just muffins; they’re a delightful journey of flavor and texture, perfectly embodying the cozy essence of the fall season. Each muffin boasts a wonderfully soft and moist pumpkin-spiced base, generously infused with aromatic notes of cinnamon, nutmeg, and the comforting warmth of pumpkin pie spice. But the true magic lies within: a luscious, sweet, and tangy cream cheese filling that creates an irresistible surprise in every single bite. Baked to perfection, these muffins rise beautifully tall, promising a satisfyingly fluffy texture and that coveted domed top.

Imagine waking up to the aroma of these freshly baked pumpkin cream cheese muffins permeating your home. They are the ideal breakfast treat, a decadent brunch addition, or a comforting snack any time of day. This recipe isn’t just delicious; it’s surprisingly straightforward, requiring simple ingredients and a mere eight steps from start to finish. Whether you’re an experienced baker or just starting out, you’ll find this recipe incredibly approachable. We’ve packed this guide with detailed tips, tricks, and illustrative process photos to ensure your muffins turn out perfectly every time. Get ready to make this your new go-to pumpkin muffin recipe for the entire autumn season and beyond!
The combination of rich pumpkin flavor and the smooth, sweet cream cheese center is what sets these muffins apart. They offer a harmonious blend of earthy spices and creamy indulgence that truly captures the spirit of fall. Forget dry, crumbly muffins; ours are designed for maximum moisture and a tender crumb, making each bite an absolute pleasure. If you’re a connoisseur of pumpkin desserts, then these cream cheese-filled pumpkin muffins are an absolute must-try. And if you’re looking for other delightful pumpkin creations, be sure to explore our Pumpkin Cream Cheese Bread for another taste of seasonal perfection.

Secrets to Baking the Best Pumpkin Cream Cheese Muffins
Achieving bakery-quality muffins at home is entirely possible with a few expert insights. Here are our top tips and tricks to ensure your pumpkin cream cheese muffins are exceptionally moist, perfectly spiced, and boast that enviable tall, domed top with a delightful cream cheese surprise in the middle.
- Maximize Pumpkin Flavor by Blotting Puree: This might sound unconventional, but it’s a game-changer! Before incorporating your pumpkin puree into the batter, spread it thinly on a dinner plate. Gently press several sheets of paper towel (using two at a time) onto the puree to absorb excess moisture. Repeat this process about 3-4 times. By removing some of the water, you concentrate the pumpkin flavor without altering the final texture of your muffins, resulting in a richer, more pronounced pumpkin taste.
- Rest Your Batter for a Better Rise: Once you’ve mixed your pumpkin muffin batter, don’t rush it into the oven. Allow the batter to sit for about 10-15 minutes while you preheat your oven and prepare your muffin pans and cream cheese filling. This brief resting period allows the gluten in the flour to relax and absorb the liquids more fully. The result? A more tender muffin crumb and a significantly improved rise, contributing to those desirable tall muffin tops.
- Strategic Muffin Liner Placement for Optimal Baking: For muffins that truly rise tall and bake evenly, resist the urge to fill every cavity of your muffin pan. Instead, place only six muffin liners in a standard 12-cup muffin pan, leaving an empty space between each one. This allows the heat to circulate more effectively around each individual muffin, promoting a stronger, more even rise and a beautifully baked exterior.
- Don’t Skimp on Filling the Liners: To achieve those wonderfully large, domed muffin tops, make sure to fill your muffin liners generously. For these pumpkin cream cheese muffins, you’ll be adding a heaping scoop of pumpkin batter, followed by the cream cheese filling. Filling the liners nearly to the top provides enough batter for the muffins to expand upwards as they bake.
- Room Temperature Ingredients are Key: For both the pumpkin muffin batter and the cream cheese filling, ensuring your dairy ingredients (butter, eggs, sour cream, buttermilk, and cream cheese) are at room temperature is crucial. This allows them to emulsify better, creating a smooth, uniform batter and a perfectly creamy filling, free of lumps. Plan ahead and pull these ingredients out of the fridge at least 30 minutes to an hour before you begin baking.





Ingredient Spotlight: What Makes These Muffins Shine
Each ingredient in this recipe plays a crucial role in creating the perfect pumpkin cream cheese muffin. Understanding why they’re chosen can help you achieve the best results and even inspire thoughtful substitutions.
For the Pumpkin Muffins:
- Pumpkin Puree: Be sure to use 100% pure pumpkin puree, not pumpkin pie filling, which contains added spices and sugar. Our blotting technique (see tips!) enhances the natural pumpkin flavor.
- All-Purpose Flour: The foundation of our muffin structure. For accuracy, always spoon and level your flour or, even better, use a kitchen scale for precise measurements. Over-measured flour can lead to dry muffins.
- Baking Powder & Baking Soda: This dynamic duo provides the lift, ensuring your muffins are light, fluffy, and rise beautifully tall.
- Pumpkin Pie Spice, Cinnamon & Nutmeg: This carefully balanced blend of spices creates that quintessential warm, autumnal flavor profile. Feel free to adjust to your personal preference for spice intensity.
- Brown Sugar: Adds moisture and a deep, caramel-like sweetness that complements the pumpkin perfectly. Light or dark brown sugar works well; dark brown sugar will give a slightly richer flavor and darker hue.
- Melted Butter: Contributes to a tender crumb and rich flavor. Ensure it’s melted and then cooled slightly before mixing to avoid cooking the eggs.
- Sour Cream & Buttermilk: These dairy ingredients are essential for a moist, tender crumb and add a subtle tang that balances the sweetness. Make sure they are at room temperature.
- Large Egg & Vanilla Extract: The egg binds the ingredients and adds richness, while vanilla enhances all the flavors.
- Coarse Sugar: A sprinkle on top before baking adds a beautiful sparkle and a delightful textural crunch to the muffin tops.
For the Cream Cheese Filling:
- Cream Cheese: Use full-fat, block cream cheese (not whipped or spreadable) at room temperature for the best consistency. This creates a rich, smooth, and stable filling.
- White Granulated Sugar: Sweetens the cream cheese to perfection.
- All-Purpose Flour: A small amount helps stabilize the cream cheese filling, preventing it from becoming too runny during baking.
- Milk & Vanilla Extract: Thin the filling slightly for easier piping and add a touch of flavor.
Baking Success: A Step-by-Step Guide
Follow these detailed steps to create your own batch of irresistible Pumpkin Cream Cheese Muffins. Precision and patience are your best friends in the kitchen!

Pumpkin Cream Cheese Muffins
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20 minutes
14 minutes
34 minutes
12 muffins
Ingredients
Pumpkin Muffins
- 2 cups All-purpose flour
- 2 tsp Baking powder
- 1/2 tsp Baking soda
- 1/2 tsp Salt
- 2 tsp Ground cinnamon
- 1 tsp Pumpkin pie spice
- 1/4 tsp Ground nutmeg
- 15 oz Pumpkin puree, 1 can of puree
- 1/2 cup Unsalted butter, melted and cooled
- 3/4 cup Brown sugar, packed light or dark
- 1 Large egg, room temperature
- 1 tsp Pure vanilla extract
- 1/4 cup Sour cream, room temperature
- 1/2 cup Buttermilk, room temperature
- Coarse sugar, like sugar in the raw
Cream Cheese Filling
- 4 oz Cream cheese, room temperature
- 2 TBSP White granulated sugar
- 1 tsp All-purpose flour
- 1 tsp Milk
- 1 tsp Pure vanilla extract
Instructions
Pumpkin Muffins
- In a large bowl, whisk together the all-purpose flour, baking powder, baking soda, salt, ground cinnamon, pumpkin pie spice, and ground nutmeg. Set this dry mixture aside. For the pumpkin puree, spread it on a dinner plate and gently press 8 sheets of paper towel (using 2 at a time) onto it to absorb excess moisture. This intensifies the pumpkin flavor.2 cups All-purpose flour, 2 tsp Baking powder, 1/2 tsp Baking soda, 1/2 tsp Salt, 2 tsp Ground cinnamon, 1 tsp Pumpkin pie spice, 1/4 tsp Ground nutmeg, 15 oz Pumpkin puree
- In a separate medium-sized bowl, combine the cooled melted butter, blotted pumpkin puree, brown sugar, room temperature egg, pure vanilla extract, room temperature sour cream, and room temperature buttermilk. Whisk until well combined. Pour these wet ingredients into the dry ingredients. Mix gently with a rubber spatula until just combined. Be careful not to overmix the batter. Allow the batter to rest for 10-15 minutes while you prepare for baking.1/2 cup Unsalted butter, 3/4 cup Brown sugar, 1 Large egg, 1 tsp Pure vanilla extract, 1/2 cup Buttermilk, 1/4 cup Sour cream
Cream Cheese Filling & Baking
- Preheat your oven to 425℉ (220℃). Line a 12-cup muffin pan with 6 muffin liners, ensuring there is an empty cup between each liner. This allows for better heat circulation and a higher rise.
- Using a large cookie scoop, fill each prepared muffin liner with a heaping scoop of pumpkin muffin batter, almost to the top. Sprinkle a generous amount of coarse sugar over the top of each muffin batter-filled liner.Coarse sugar
- In a small bowl, use a hand mixer to beat the room temperature cream cheese, white granulated sugar, all-purpose flour, milk, and pure vanilla extract on high speed until the mixture is completely smooth and creamy.4 oz Cream cheese, 2 TBSP White granulated sugar, 1 tsp All-purpose flour, 1 tsp Milk, 1 tsp Pure vanilla extract
- Transfer the cream cheese filling into a piping bag (or a sturdy Ziploc bag with a corner snipped off). Insert the tip of the piping bag about one-third of the way down into the center of each muffin batter-filled liner. Gently squeeze the bag to pipe a dollop of cream cheese filling into the center, allowing it to reach close to the top. You should use all of the filling for the 12 muffins.
- Bake the muffins in the preheated 425℉ (220℃) oven for 8 minutes. Then, without opening the oven door, reduce the oven temperature to 350℉ (175℃) and continue baking for another 6-8 minutes, or until a toothpick inserted into the pumpkin muffin portion (avoiding the cream cheese filling) comes out clean.
- Allow the muffins to cool in the hot muffin pan for about 10 minutes before carefully transferring them to a wire rack to cool completely. These muffins are truly at their best when served chilled, so store any cooled muffins in an airtight container in the refrigerator.
Notes
High Altitude Baking: If you are baking at a high altitude, you may need to add an extra 2 tablespoons of all-purpose flour to the muffin batter to compensate for the lower atmospheric pressure.
Room Temperature Dairy: For optimal results, pull out all dairy ingredients (butter, cream cheese, sour cream, buttermilk, eggs) from the refrigerator at least 30 minutes to 2 hours before you plan to start baking. This ensures they blend smoothly and contribute to a uniform batter and filling.
Carbohydrates: 36g,
Protein: 4g,
Fat: 13g,
Saturated Fat: 8g,
Polyunsaturated Fat: 1g,
Monounsaturated Fat: 3g,
Trans Fat: 0.3g,
Cholesterol: 34mg,
Sodium: 262mg,
Potassium: 152mg,
Fiber: 2g,
Sugar: 18g,
Vitamin A: 5927IU,
Vitamin C: 2mg,
Calcium: 96mg,
Iron: 2mg
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Storage and Serving Suggestions
To enjoy these magnificent pumpkin cream cheese muffins at their absolute best, proper storage is essential. Since they contain a cream cheese filling, these muffins are best stored in the refrigerator. Place them in an airtight container once they have completely cooled to maintain their freshness and prevent them from drying out. They will stay fresh for up to 3-4 days in the fridge. For a delightful treat, try gently warming them for a few seconds in the microwave to slightly soften the pumpkin base, or enjoy them chilled straight from the refrigerator – many find the cold cream cheese filling especially refreshing!
These muffins are incredibly versatile. Serve them as a special breakfast or brunch item alongside a warm cup of coffee or tea. They also make a fantastic dessert, particularly when served with a dusting of powdered sugar or a dollop of whipped cream. For a truly seasonal experience, pair them with a homemade apple cider or a pumpkin spice latte.
Variations to Explore
While this recipe for Pumpkin Cream Cheese Muffins is perfect as is, feel free to get creative and customize them to your liking:
- Add Chocolate Chips: Fold 1/2 to 1 cup of mini chocolate chips or regular chocolate chips into the pumpkin muffin batter for an extra layer of sweetness and texture. If you love this combination, be sure to try our Chocolate Chip Pumpkin Muffins!
- Nutty Crunch: Incorporate 1/2 cup of chopped pecans or walnuts into the batter for a delightful nutty crunch.
- Spice it Up: If you prefer an even bolder spice profile, consider adding a pinch of ground ginger or cloves to the pumpkin muffin batter.
- Streusel Topping: For an extra special touch, whip up a simple streusel topping with flour, brown sugar, butter, and a dash of cinnamon, and sprinkle it over the muffins before baking.
- Different Fillings: While cream cheese is heavenly, you could experiment with other fillings, such as a dollop of apple butter or a swirl of Nutella, though baking times and consistency may vary.

We hope you thoroughly enjoy baking and savoring these delightful Pumpkin Cream Cheese Muffins. They truly capture the essence of fall in every bite, from the warm spices to the creamy, sweet filling. Don’t forget to explore our other delicious fall recipes, including our comforting Pumpkin Banana Muffins.
If you loved this recipe, please leave astar review and share your feedback! We always love hearing from you. Don’t forget to tag us on Instagram @stephaniesweettreats with your creations. For more inspiring baking ideas and delicious recipes, be sure to follow us on Pinterest.
