These amazing Pumpkin Cream Cheese Muffins are the perfect fall treat! These perfectly moist pumpkin muffins are filled with a creamy, luscious cream cheese filling and topped with sweetened and spiced pumpkin seeds. A delicious addition to your brunch (or dessert!) menu this holiday season.
Love all things pumpkin? Make sure to try my Pumpkin Muffins with Cinnamon Streusel and Pumpkin Cake with Salted Caramel Frosting!
If you’ve been lusting after those Starbucks pumpkin cream cheese muffins then I’m here to give you some great news – you can totally make your very own Pumpkin Cream Cheese Muffins from the comfort and convenience of your kitchen!
These pumpkin muffins are super moist, full of delicious pumpkin flavor with an irresistible sweet cream cheese filling and spiced pumpkin seeds sprinkled on top! They’re in a class of their own – perfect for the holidays or anytime you have a craving for a decadent muffin!
More Scrumptious Muffin Recipes
Love muffins as much as we do? The pumpkin cheesecake muffins are exceptional and here are some more of our favorites:
- Pumpkin Spice Doughnut Hole Muffins
- Raspberry Lemon Muffins
- Cranberry Orange Muffins
- Morning Glory Muffins
- Pumpkin Muffins with Cinnamon Streusel
What You’ll Need
Let’s take a quick look at what you’ll need to make these Pumpkin Cheesecake Muffins and, as always, you can find the full, printable recipe card at the end of this post.
For the Pumpkin Muffins
- pumpkin puree – use canned pumpkin puree not pumpkin pie filling for this recipe.
- vegetable oil – canola oil can also be used.
- brown sugar and granulated sugar – a combination of brown sugar and granulated sugar gives the perfect amount of sweetness and flavor.
- whole milk – whole milk gives the best results but lowfat milk can be used in a pinch.
- eggs – room temperature is best.
- vanilla extract – or vanilla bean paste, use the real stuff for best results.
- all purpose flour – this provides the structures for these muffins.
- pumpkin pie spice – really takes these muffins to the next level and makes them taste like pumpkin.
- baking powder and baking soda – our leaveners for this recipe.
- salt – for flavor and balance.
For the Cream Cheese Filling
- cream cheese – softened slightly
- all purpose flour – creates a thicker filling that won’t drip when you’re enjoying these muffins.
- granulated sugar – to sweeten the cream cheese.
- sour cream – adds a tangy element that is traditional in cheesecake.
- vanilla extract – or vanilla bean paste, use the good stuff or make my homemade vanilla extract.
- sea salt – or kosher salt can also be sued.
For the Pumpkin Seed Topping
- pumpkin seeds – you can find these in the nuts aisle typically or I buy my pumpkin seeds online.
- pumpkin pie spice – for flavor and spice.
- granulated sugar – a little sweetness, this is optional.
How To Make Pumpkin Cream Cheese Muffins
These muffins come together rather quickly. There are three components: the pumpkin muffins, the cheesecake or cream cheese filling and the pumpkin seeds. Let’s take a quick look at how to make them:
For the Pumpkin Muffins:
- Preheat the oven and line a muffin pan with parchment liners.
- Whisk together the oil and pumpkin puree. Whisk in brown sugar and granulated sugar and finally whisk in the milk, eggs and vanilla extract.
- Whisk together the flour, pumpkin pie spice, baking powder, baking soda and salt.
- Fold the dry ingredients into the wet ingredients and stir just until combined.
- Scoop into the prepared muffin pan.
- With a spoon or knife, press a hole into the batter of each muffin, making way for the cream cheese filling.
Prepare the Cream Cheese Filling
- Beat cream cheese until creamy and smooth.
- Beat in the flour, granulated sugar, sour cream, vanilla extract and salt.
- Transfer to a large resealable bag, cut one corner off the bottom of the bag and fill the centers of each muffin with the cream cheese filling.
Spiced Pumpkin Seeds
- Toss the pumpkin seeds together with the pumpkin pie spice and sugar.
- Top each muffin with a few of the pumpkin seeds.
- Bake for 18 to 22 minutes.
- Let the muffins cool before transferring to a cooling rack.
Recipe Notes:
When testing to see if the muffins are done, insert a toothpick into the pumpkin part of the muffin. It should come out clean with a few moist crumbs. Don’t insert it into the cream cheese filling.
Storage Information
While most muffins can be stored at room temperature in an airtight container for a couple of days, since these pumpkin cream cheese muffins contain a cheesecake filling, I suggest that they be stored in the refrigerator for up to 5 days in an airtight container.
If you removed the parchment muffin liners already, then place a sheet of wax paper or parchment paper down on the bottom of the container so that the muffins don’t stick to the container. If the liners are still on, then skip this step.
When you’re ready to enjoy your leftover pumpkin muffins, either serve them chilled straight out of the refrigerator, or bring them to room temperature before serving. You can’t reheat these muffins in the oven or microwave like you might with other muffins due to the cream cheese filling, so just keep that in mind.
Can I Freeze These Muffins?
Absolutely! If you want to make these scrumptious muffins ahead of time or wish to store leftovers that you know you won’t eat for a while then go ahead and store the muffins in your freezer for up to 3 months.
Flash freezing your muffins on a baking tray in the freezer for about 2 hours is a good idea before placing them in an airtight container or Ziploc bag. It’ll help prevent the muffins from sticking to each other in storage, especially if you’ve opted to stack them or place them in a freezer bag.
Thaw your frozen pumpkin cream cheese muffins overnight in the refrigerator and then either serve them chilled or bring them to room temperature prior to serving.
Can I Use Pumpkin Pie Filling Instead of Pumpkin Puree?
The short answer is no, definitely not and here’s why: Pumpkin puree (aka canned pumpkin) is just cooked pumpkin without any additional ingredients such as sugar or spice. Pumpkin pie filling, on the other hand, contains added sugar, spices and other ingredients to extend its shelf life.
You’ll see then that the two are different and can’t just be used interchangeably without having to carefully adjust the ingredients already called for in this recipe. If you were to use pumpkin pie filling for these muffins, they would definitely be overly sweet and spiced and the texture of your muffins may even be affected.
Trish’s Tips and Tricks
- Never overmix your muffin batter – this applies to any batch of muffins you make. If you do, your muffins will become tough and dense instead of soft and moist.
- You can make the small holes in your muffin batter with the back of a spoon to make room for the cream cheese filling.
- It’s going to be much easier to manage the cream cheese filling if you add it to a piping bag or a Ziploc bag, cutting one corner of the bag off. You’ll then be able to insert the cut corner deep within the hole of the muffin batter to squeeze the cream cheese filling into. It would be quite tricky to do this with a teaspoon – I don’t recommend that.
- I’ve spiced my pumpkin seeds for these muffins but you can leave them plain if you’d prefer.
- You could easily double the quantity of these muffins if you’re catering to a larger crowd or preparing for busy times ahead.
You could easily double the quantity of these muffins if you’re catering to a larger crowd or preparing for busy times ahead.
More Brunch Favorites
How To Make Pumpkin Cream Cheese Muffins
Pumpkin Cream Cheese Muffins
Ingredients
Pumpkin Muffins
- 1 cup pumpkin puree
- ⅓ cup vegetable oil
- ½ cup brown sugar
- ½ cup granulated sugar
- ¼ cup whole milk
- 2 large eggs
- 1 teaspoon vanilla extract or vanilla bean paste
- 2 cups all purpose flour
- 2 teaspoons pumpkin pie spice
- 1 teaspoon baking powder
- 1 teaspoon baking soda
- ¼ teaspoon salt
Cream Cheese Filling
- 8 ounces cream cheese softened slightly
- 1 tablespoon all purpose flour
- ½ cup granulated sugar
- 1 teaspoon sour cream
- 1 teaspoon vanilla extract or vanilla bean paste
- ½ teaspoon sea salt or kosher salt
Topping
- ¼ cup pumpkin seeds
- 1 teaspoon pumpkin pie spice
- ¼ teaspoon granulated sugar
Instructions
For the Pumpkin Muffins:
- Preheat the oven to 375°F and line a muffin pan with parchment liners. If not using parchment, spray liners with a nonstick cooking spray. Set aside.
- In a large bowl, whisk together the vegetable oil and pumpkin puree. Add the brown sugar and granulated sugar and whisk to combine. Next, whisk in the milk, eggs and vanilla extract. Set aside.
- In a medium bowl, whisk together the all purpose flour, pumpkin pie spice, baking powder, baking soda and salt.
- Fold the dry ingredients into the wet pumpkin mixture and stir just until combined.
- Scoop the batter into the prepared muffin pan almost to the top.
- With a spoon or knife, press a hole or indentation into the batter of each muffin, making way for the cream cheese filling.
For the Cream Cheese Center:
- In a large bowl or the bowl of a stand mixer, add the cream cheese and beat until creamy.
- Add the flour, granulated sugar, sour cream, vanilla extract and salt and continue beating until fully combined.
- Transfer the cream cheese mixture into a large resealable bag and press the mixture into one corner. Cut one corner off the bottom of the bag and fill the centers of each muffin with the cream cheese filling.
Spiced Pumpkin Seeds:
- In a small bowl, toss the pumpkin seeds together with the pumpkin pie spice and sugar.
- Top each muffin with a few of the pumpkin seeds.
- Bake for 18 to 22 minutes. Insert a toothpick into the pumpkin part of the muffin. It should come out clean with a few moist crumbs. Don’t insert it into the cream cheese filling.
- Let muffins cool for 10 minutes in the muffin pan before transferring to a cooling rack.
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