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Pumpkin Cheesecake Muffins are filled with a hidden cheesecake center inside a moist, pumpkin muffin laced with pumpkin spice and topped with cinnamon sugar.

About this time of year, I start counting down the days until brisk Fall air drives away the icky sticky heat. I’ve been known to start wearing my boots before this happens in an attempt to will the cool to come. Making pumpkin things before pumpkin time is my food equivalent of such a protest against the weather!

So if you’re like me, and are looking for a rich spicy muffin to transport you to flannel and vest wearing days with rosy cheeks, you need this pumpkin muffin recipe in your life! Bonus: filling them with the cheesecake is extra fun for kids, and you’ll have some coffee shop worthy muffins without the extra price.

Pumpkin Cheesecake Muffins

tower of pumpkin muffins and cross section of pumpkin muffins on plate with text overlay

Why you’ll love these pumpkin muffins

All the pumpkin spice: Using my homemade pumpkin spice blend and a little of my homemade vanilla sugar, you won’t believe how much flavor these muffins have. If you crave these warm cozy flavors, we got you covered.
Cheesecake!: Sometimes a slice of cheesecake is too rich, but a cheesecake filling like this one can bring some extra tang that balances out the sweetness perfectly.
Secret flavor in the filling: While 1 tsp of whiskey doesn’t seem like a lot, whiskey will boost the flavor of the pumpkin spice in a way that plain vanilla will not. If you have it on hand, use it!
Simple cinnamon sugar: There’s few baked goods I won’t top with streusel, but sometimes it’s nice to do something simpler. Here the cinnamon sugar makes an intriguing crust on top the muffins and gives them a little sparkle.

Ingredients for pumpkin muffins

Muffins

All-purpose flour
Brown sugar
Vanilla sugar (homemade or Native Vanilla vanilla sugar)
Baking powder
Pumpkin pie spice: (homemade or store bought)
Salt
Butter
Eggs
Canned pumpkin (not pumpkin pie filling)
Milk

Filling

Cream cheese, softened
Powdered sugar
Butter
Whiskey or vanilla paste
Pumpkin spice blend

Topping

Granulated sugar
Cinnamon

Pro tips for making the best pumpkin cheesecake muffins

Beat the filling smooth: No need for a mixer here; just keep smooshing everything together with a fork until things are smooth. A smooth filling will get you the best texture for the cheesecake.
Chill the filling: After your filling is smooth, pop it into the fridge while you make the muffins. The brief chilling time will firm up the butter and cream cheese a bit, making it easier to scoop into the muffin tins.
Cool the muffins in the oven: The filling adds extra moisture to the muffin that may make testing a little confusing as the filling will still be liquid. Turn the heat off as soon as the muffins bounce back when touched in the middle, then allow the muffins to cool briefly in the oven. This will firm everything up without overbaking the muffins.

Pumpkin Cheesecake Muffins

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Author: Elizabeth Farr
Total Time: 40 minutes
Yield: 12 muffins

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Description

Moist pumpkin spicy muffins with a simple cheesecake filling topped with cinnamon sugar. This muffin has all the Fall feels you wish for in the dead heat of Summer!

Ingredients

Scale

Filling

4 oz cream cheese, softened (113 g)
½ cup powdered sugar (60 g)
2 Tablespoons butter (28 g)
1 teaspoon whiskey or vanilla paste
1/2tsp pumpkin spice blend

Muffins

2 cups flour (260 g)
1/2 cup light brown sugar (106 g)
1 Tablespoon vanilla sugar (homemade or Native Vanilla vanilla sugar)
2 tsp baking powder
1 tsp pumpkin pie spice
1/2 tsp salt
5 Tablespoons butter, melted (70 g)
2 eggs
1 cup canned pumpkin (not pumpkin pie filling)(244 g)
3/4 cup milk (177 mL)

Topping

2 Tablespoons granulated sugar (25 g)
1 teaspoon ground cinnamon or pumpkin pie spice

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Instructions

Preheat the oven to 400 F (205 C).
Brush a 12 cavity muffin pan with 1 tablespoon of melted butter.
Beat the cheesecake filling ingredients together with a fork until smooth. Put the bowl into the fridge while you make the muffins.
Whisk the flour, sugar, baking powder, baking soda, pumpkin pie spice and salt in a large mixing bowl.
In another bowl, mix the melted butter, eggs, milk, pumpkin and vanilla.
Make a well in the dry ingredients and pour in the pumpkin mixture, then stir everything together until the flour is just moistened. Be sure to scrape down to the bottom of the bowl as there’s usually flour hanging out that you missed!
Spoon a little batter into the prepared muffin cups to cover the bottom of each cavity, then cover it with a rounded spoonful of filling. Cover the filling with more batter until each well of the tin is near the top of the tin.
Mix the sugar and cinnamon, then sprinkle generously over the top of each muffin.
Bake the muffins for 24 minutes until a toothpick inserted into the center comes out clean or the middle of a muffin springs back when you touch it.
Turn off the oven, then prop the oven door open a crack, leaving the muffins in the oven. Remove the muffins after the 5 minutes, then let them cool on a wire rack.
Keep the muffins in the fridge in a covered container for up to 5 days. Reheat them in the microwave, and serve them with good coffee!