Pumpkin Cream Cheese Muffins
These Pumpkin Cream Cheese Muffins pair the cozy flavour of pumpkin with a sweet-and-tangy cream cheese filling with delicious results. Crunchy pepitas are the perfect finishing touch!
It turns out I have a bit of a weakness for pumpkin muffins. Over the years, I’ve shared vegan pumpkin muffins, pumpkin banana muffins, and pumpkin chocolate chip muffins—but if you’re looking for a pumpkin muffin with a little bite of cheesecake in the middle, these pumpkin cream cheese muffins are for you!
The cream cheese filling really takes a basic pumpkin muffin to the next level, adding a creamy texture and tangy flavour that’s the perfect complement to the rest of the muffin. These pumpkin cream cheese muffins feel like something you’d snack on at your favourite coffee house while sipping on a pumpkin spice matcha latte!
Why You’ll Love This Pumpkin Cream Cheese Muffin Recipe
- Cozy pumpkin spice flavour. If you’re the type to get excited about pumpkin spice season (guilty!), you’ll love these pumpkin cream cheese muffins. The warm blend of spices combined with the earthy pumpkin flavour is irresistible.
- Tangy cream cheese. A creamy, tangy, cheesecake-like filling adds an extra layer of flavour and texture to the muffins.
- Vegan with an easy gluten-free option. These muffins are perfect for anyone following a vegan lifestyle, and easily made gluten-free.
Notes on Ingredients
Scroll down to the recipe card to find the ingredient quantities and recipe instructions.
- All-purpose flour – Swap in your favourite measure-for-measure gluten-free flour to make gluten-free pumpkin cream cheese muffins.
- Baking powder and baking soda
- Spices – Cinnamon and pumpkin pie spice bring warm, cozy flavour.
- Sea salt
- Sugar – Use brown sugar, cane sugar, or coconut sugar.
- Pumpkin puree – Be sure to buy pumpkin puree, not pumpkin pie mix or filling, which is sweetened.
- Oil – I use olive oil.
- Nondairy milk – Any vegan milk will work as long as it’s unflavoured.
- Vanilla extract
- Pumpkin seeds or oats – For topping.
For the Cream Cheese Filling:
- Vegan cream cheese – Let this come to room temperature.
- Powdered sugar – Also known as confectioners’ sugar.
- Vanilla extract
What Is the Best Vegan Cream Cheese for Baking?
While I love it on a bagel, I don’t recommend Miyoko’s for baking because it tends to get grainy in the oven. Kite Hill Cream Cheese is my favourite for any recipe that needs to be baked.
How to Make Pumpkin Cream Cheese Muffins
- Prepare. Preheat your oven to 425°F and grease or line a muffin pan.
- Mix the wet ingredients. Beat the sugar, pumpkin puree, and oil in a mixing bowl (or the bowl of a stand mixer) for 2 to 3 minutes. Mix in the milk and vanilla extract, scraping down the sides of the bowl as needed.
- Finish the batter. Add the dry ingredients to the bowl and slowly mix together on low speed, then medium speed, until fully incorporated. Divide the muffin batter into 10 muffin cups.
- Make the filling. Use a stand mixer or hand mixer on medium speed to beat the softened cream cheese, powdered sugar, and vanilla extract for about 2 minutes, or until the mixture is fluffy.
- Add the filling. Transfer the cream cheese mixture to a piping bag. Place the tip of the piping bag into the centre of each muffin, then press down to squeeze, pulling up slowly until you reach the top of the muffin.
- Bake. Sprinkle oats or pepitas on top, as desired, then add water to the empty muffin cups. Bake for 5 minutes at 425°F, then reduce the temperature to 350°F degrees and bake for another 15 minutes, or until a toothpick inserted into a muffin comes out clean.
- Cool. Let the pumpkin cream cheese muffins cool in the pan for about 5 minutes, then transfer them to a wire rack to finish cooling.
Tips for Success
- Fill the empty muffin cups with water. This is my little trick for ensuring even baking and a nice rise. The steam from the water helps create a moist environment in the oven, leading to perfect muffins.
- Don’t overmix the batter. This can result in tough, dense pumpkin cream cheese muffins. Mix until all the ingredients are just incorporated.
- Use room temperature cream cheese for the filling. This makes it easier to mix and ensures a smooth and creamy filling.
- Drain the liquid from homemade pumpkin puree. You can use homemade pumpkin puree if you’d like, but it tends to be a little wetter than the canned kind. To remedy this, line a fine mesh colander with paper towels, then let the pumpkin puree sit in there for 30 minutes before using it in this recipe.
- Use a cookie dough scoop. This is the best way to make sure all of the muffins have the same amount of pumpkin muffin batter!
- Add mini chocolate chips to the cream cheese filling for a chocolatey twist.
- Drizzle melted dark chocolate over the muffins after baking for an indulgent treat.
- Swap the pumpkin puree for canned butternut squash puree—the taste is the same, but this is a nice trick for those times when your grocery store is sold out of canned pumpkin!
- Swap chopped nuts, such as pecans or walnuts, for the pepitas for a more nutty flavor.
I love serving muffins alongside a savoury breakfast option like fluffy tofu scramble or easy vegan quiche. If you’re enjoying these for a weekday breakfast, simply pair them with some fresh fruit or a bowl of vegan yogurt.
How to Store
Pumpkin cream cheese muffins will keep for up to 2 days in an airtight container at room temperature, or up to a week in the refrigerator.
Can I Freeze This Recipe?
You can freeze these muffins for up to 3 months. Allow them to cool completely before placing them in freezer-safe bags or containers. When ready to eat, thaw overnight in the refrigerator or microwave on low power until warmed through.
More Vegan Muffin Recipes
- Vegan Lemon Poppyseed Muffins
- Double Chocolate Banana Muffins
- Vegan Zucchini Muffins
- The Best Vegan Blueberry Muffins
- Apple Streusel Muffins
Enjoy friends! If you make this pumpkin cream cheese muffin recipe, please snap a photo and tag #jessicainthekitchen on Instagram! We’d also love it if you would leave a comment below, and give the recipe a rating! Thanks so much!
Pumpkin Cream Cheese Muffins
- 2 cups all purpose flour, (240g)
- 1 tablespoon baking powder, (14g)
- 1/2 teaspoon baking soda, (3g)
- 1 teaspoon cinnamon
- 1 teaspoon pumpkin pie spice
- 1/2 teaspoon sea salt
- 1 cup sugar, (200g) brown sugar, cane sugar, coconut sugar – any kind of granulated sugar
- 1 cup pumpkin puree, (244g) not pumpkin pie filling
- 1/3 cup oil, (66g) any oil (I prefer olive oil)
- 1/2 cup nondairy milk + 2 tablespoons, (150mL) any vegan milk works
- 2 teaspoons vanilla extract
- 2 tablespoons pumpkin seeds or oats for topping
Cream Cheese Filling
- 8 oz vegan cream cheese, room temperature
- 1/4 cup powdered sugar
- ½ teaspoon vanilla extract
- Preheat oven to 425°F/220°C. Spray a muffin pan with non-stick flour spray or rub with vegan butter, or line with muffin/cupcake liners.
- In a bowl of a mixer or with a hand mixer on medium (or using a whisk), mix the sugar, pumpkin puree and oil together for about 2 to 3 minutes. Add in the milk and vanilla extract and mix together for another minute until fully incorporated, scraping down the sides.
- Into the wet batter add in the sea salt, pumpkin pie spice, cinnamon and then sift the flour, baking powder and baking soda. You want to ensure your flour, baking powder and baking soda are free of clumps so I would recommend sifting them in with a sifter, sieve or a strainer.
- Slowly mix together on low speed, then back to medium, until fully incorporated, for another 2 minutes. Scrape down the sides of the bowl as needed.
- Scoop the muffin batter (I use a large cookie scoop or a 1/3 cup measuring cup) equally into 10 muffin cups/holes.
Cream Cheese Filling
- In a bowl add the softened cream cheese, powdered sugar and the vanilla extract. Using a stand mixer or with a hand mixer or with a whisk, throughly mix all the ingredients together on medium speed until it’s all incorporated and fluffy for about 2 minutes.
Putting it Together and in Oven
- Scoop the cream cheese mixture into a piping bag and cut about ⅓ inch wide hole out. Squeeze the cream cheese down all the way to the tip. To help scoop it into the bag I place my piping bag in a drinking glass to get it as wide open as possible then scoop it in a lot easier.
- Place the tip of the piping bag into the centre of each muffin. Press down to squeeze, pulling up slowly until you reach the top of each muffin. Evenly distribute the batter throughout each muffin, about 1.5 tablespoons in each muffin. Don’t place the bag into the bottom of the batter. When pulling out you can do a little dollop at the top or a swirl.
- If you have any excess batter feel free to push the tip back into the centre of the muffin batter and squeeze some remainder throughout each.
- Add your desired toppings on top of the muffins – I usually do 1 tablespoon oats and 1 tablespoon pumpkin seeds/pepitas, (or 2 tablespoons of only pumpkin seeds or only oats) mix them, then sprinkle them over, pressing in slightly to the top and around the cream cheese hole.
- Place water in the empty muffin cups. Don’t skip this step! It ensures that the muffins bake evenly and rise beautifully
- Add your muffins into the oven. Bake for 5 minutes at 425°F/220°C, then leaving the muffins in the oven and not opening the door, reduce the temperature to 350°F/180°C degrees and bake for another 15 minutes until a toothpick inserted into a muffin comes out clean. Remove from oven and allow to cool in pan for about 5 minutes. Remove (I just use the same toothpick or a knife) and place on a wire rack to cool completely. Allowing the cupcakes to cool completely ensures
- For the vegan cream cheese, I don’t recommend miyokos for this (it gets grainy) but kite hill cream cheese works incredibly here
- To store: Pumpkin cream cheese muffins will keep for up to 2 days in an airtight container at room temperature, or up to a week in the refrigerator.
- To freeze: You can freeze these muffins for up to 3 months. Allow them to cool completely before placing them in freezer-safe bags or containers. When ready to eat, thaw overnight in the refrigerator or microwave on low power until warmed through.
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