Homemade Pumpkin Muffins With Cream Cheese Filling
What is more fall than a pumpkin muffin with cream cheese filling, a cup of tea, and a book?! These pumpkin muffins have a delicious homemade taste, aren’t sweet, and have the perfect balance of fall spices. Plus, the cream cheese filling is tangy and the perfect combination!


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Pumpkin muffins with cream cheese filling
You’re reading the blog post of someone who is not a fan of the PSL (pumpkin spice latte). I’ll admit it, I wish I liked this fall drink, but although it’s not for me, pumpkin baked goods surprisingly are.
…Maybe it’s not that surprising. Most PSL’s are made with pumpkin pie spice, not real pumpkin. There is a taste difference there. So if you’re a fan of pumpkin in any form, this recipe is for you. The combination of real pumpkin puree and warm spices is delicious and perfect for a fall morning (or anytime the muffin craving strikes).

The ingredients list
Make sure to check that you have all of the listed ingredients before baking! It’s not fun to have to run out to the store mid-bake (trust me I know).
- Cream cheese
- Granulated sugar
- Eggs
- Vanilla paste (or extract)
- All-purpose flour
- Baking soda
- Salt (I use Kosher)
- Ground cinnamon
- Ground ginger
- Ground cloves
- Canned pumpkin puree (I use Libby’s or Trader Joes)
- Buttermilk
- Pumpkin seeds (I’ve used both salted and unsalted and it’s tasty either way)
Are they sweet?
Although these muffins may be inspired by a certain coffee chain, they are not sweet. They are more of a savory taste with a sweetness and tanginess coming from the cream cheese filling.
Jumbo v.s. standard
For this pumpkin muffin recipe, I actually recommend using a jumbo muffin tin. The ratio between the cream cheese filling and the muffin works really well.
Standard muffins work too, it’s just a different ratio! You can check out the pictures on this blog post to see what the jumbo muffins look like.

How to make pumpkin muffins
- Make the cream cheese filling first. Transfer the filling into the fridge while you make the muffin batter.
- Prepare. Preheat the oven to 375℉ (190℃). Prepare a standard muffin tin with liners, or a jumbo muffin tin. These are nice standard liners that are perfect for muffins. These liners are best for jumbo size!
- Make the batter. In a large bowl, add the flour, sugar, baking soda, salt, ground cinnamon, ground ginger, and ground cloves. Whisk and set aside. In a different bowl, add the pumpkin puree, canola oil, buttermilk, eggs, and vanilla paste. Whisk together until smooth. Fold the wet ingredients into the dry with a spatula until there are no flour streaks left.
- Bake.
- Standard muffin tin: Scoop batter halfway into the prepared muffin cups. Add 1 tsp of the cream cheese filling. Top with more batter until it’s close to the top of the muffin cup. Cover the cream cheese as best you can, it’s okay if some shows. Sprinkle pumpkin seeds on top.
- Jumbo muffin tin: Scoop batter halfway into the prepared muffin cups. Add 2-3 tsp of the cream cheese filling. Top with more batter until it’s close to the top of the muffin cup. Cover the cream cheese as best you can, it’s okay if some shows. Sprinkle pumpkin seeds on top.
- Bake for 25 minutes. Check to see if the muffin tops are high and domed, and look matte.
- Cool. Let the muffins cool in the tin for 10 minutes, then transfer to a wire cooling rack. Muffin domes may deflate a little.
Storing and freezing
Store these in an airtight container at room temperature for a day. Move into the fridge after (because of the cream cheese) and store up to 5 days.
Muffins can be frozen for up to two months in a freezer safe, tightly sealed bag. Let the muffin thaw before serving.
Tip: these pumpkin muffins are tasty in a toaster oven for a few minutes, with a little butter.
RECIPE CARD
Homemade Pumpkin Muffins With Cream Cheese Filling
Equipment
- large mixing bowl
Ingredients
Cream Cheese Filling
- 4 oz cream cheese, softened to room temperature (226g)
- ½ cup powdered sugar (57g)
- 1 tsp vanilla paste (or vanilla extract)
Pumpkin Muffins
- 1 ½ cups all-purpose flour (150g)
- 1 cups granulated sugar (250g)
- ¾ tsp baking soda
- ¾ tsp salt (I use kosher)
- ¾ tsp ground cinnamon
- ½ tsp ground ginger
- ¼ tsp ground cloves
- 1 cup canned pumpkin puree (I use Libby's) (244g)
- ¼ cup + 2 tbsp canola oil or vegetable oil (82g)
- ¼ cup buttermilk (57g)
- 2 large eggs (100g)
- 1 tsp vanilla paste (or vanilla extract)
- pumpkin seeds (I've used roasted unsalted, and roasted salted and both were tasty)
Instructions
Cream Cheese Filling
- In the bowl of a stand mixer fitted with a paddle attachment or a large bowl with a hand mixer, add the cream cheese. Whip on high speed for 30 seconds. Add the powdered sugar and mix on medium speed until smooth.4 oz cream cheese, softened to room temperature, ½ cup powdered sugar, 1 tsp vanilla paste (or vanilla extract)
- Transfer the cream cheese filling into the refrigerator to chill while you make the muffin batter. Filling can be stored in the refrigerator for up to a week in an airtight container.
Pumpkin Muffins
- Preheat the oven to 375℉ (190℃). Prepare a standard muffin tin with liners, or a jumbo muffin tin. If you don't have liners, spray the wells with cooking spray.
- In a large bowl, add the flour, sugar, baking soda, salt, ground cinnamon, ground ginger, and ground cloves. Whisk and set aside.1 ½ cups all-purpose flour, 1 cups granulated sugar, ¾ tsp baking soda, ¾ tsp salt , ¾ tsp ground cinnamon, ½ tsp ground ginger, ¼ tsp ground cloves
- In a large bowl, add the pumpkin puree, canola oil, buttermilk, eggs, and vanilla paste. Whisk together until smooth.1 cup canned pumpkin puree (I use Libby's), ¼ cup + 2 tbsp canola oil or vegetable oil, ¼ cup buttermilk, 2 large eggs, 1 tsp vanilla paste
- Fold the wet ingredients into the dry with a spatula until there are no flour streaks left.
- Standard muffin tin: Scoop batter halfway into the prepared muffin cups. Add 1 tsp of the cream cheese filling. Top with more batter until it's close to the top of the muffin cup. Cover the cream cheese as best you can, it's okay if some shows. Sprinkle pumpkin seeds on top.
- Jumbo muffin tin: Scoop batter halfway into the prepared muffin cups. Add 2-3 tsp of the cream cheese filling. Top with more batter until it's close to the top of the muffin cup. Cover the cream cheese as best you can, it's okay if some shows. Sprinkle pumpkin seeds on top.pumpkin seeds
- Bake for 25 minutes. Check to see if the muffin tops are high and domed, and look matte. If they are still wet looking, add 5 more minutes.
- Let the muffins cool in the tin for 10 minutes, then transfer to a wire cooling rack. Muffin domes may deflate a little.
Notes
- Helpful tools: Standard liners | Jumbo liners

