Pumpkin Cream Cheese Muffins

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 vegan 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. They’re a great vegan alternative to Starbucks, and even better since they’re homemade!

Why Pumpkin Cream Cheese Muffins Belong On Your Fall Bake List

• If you’re the type to get excited about pumpkin spice season (guilty!), you’ll love the combination of real pumpkin purée and cozy pumpkin spice flavour in these pumpkin cream cheese muffins. It’s irresistible.
• The creamy, tangy, cheesecake-like filling tastes like cream cheese frosting and adds another layer of flavour and texture.
• These muffins are vegan with an easy gluten-free option, but everyone enjoys them.

Notes on Ingredients

Gather the following ingredients to make these decadent pumpkin cream cheese muffins from scratch (see the recipe card for the exact recipe amounts):

• 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 – I use both to ensure these vegan pumpkin muffins come out tall and fluffy. Check the dates on the packages, and if your leavening is old or expired, I recommend buying fresh.
• Spices – Cinnamon and pumpkin pie spice bring warm, cozy flavour.
• Sugar – Use brown sugar, cane sugar, or coconut sugar.
• Pumpkin puree – Be sure to buy canned 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 – Make sure it’s the real deal. Artificial vanilla tastes… well, artificial.
• Pumpkin seeds or oats – For topping. You could also garnish these muffins with chopped walnuts or pecans, or leave them plain.

For the Cream Cheese Filling

• Vegan cream cheese – Let this come to room temperature. Kite Hill Cream Cheese is my favourite for any treat that needs to be baked. I don’t recommend Miyoko’s for baking. While I love it on a bagel, it tends to get grainy in the oven.
• Powdered sugar – Also known as confectioners’ sugar.
• Vanilla extract

How to Make Pumpkin Cream Cheese Muffins

The pumpkin muffin batter comes together in one bowl, so you only need one more for making the cream cheese filling! These muffins are as easy to make as a loaf of pumpkin bread, and the house smells just as amazing while they bake.

• 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 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 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 the Best Pumpkin Muffins

• 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!

Variations

• Add mini chocolate chips to the cream cheese filling for a chocolatey twist. Or, fold chocolate chips into the muffin batter to make pumpkin chocolate chip muffins filled with cream cheese.
• 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.

Serving Pumpkin Cream Cheese Muffins

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, take them to go with some fresh fruit or a bowl of vegan yogurt. Or, for a cozy fall brunch, pair your muffins with a hashbrown casserole.

How to Store

• Store airtight. 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.
• 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.

More Vegan Pumpkin Recipes

I have so many delicious pumpkin recipes ready for fall baking! These are more ideas.

• Pumpkin Pie Overnight Oats
• Pumpkin Pancakes
• Vegan Pumpkin Pie
• Pumpkin Waffles
• Vegan Chocolate Chip Pumpkin Bread
• Vegan Pumpkin French Toast
• Pumpkin Brownies
• Vegan Pumpkin Sheet Cake

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!