Pumpkin Cream Cheese Muffins

Like a delicious pumpkin roll, these pumpkin cream cheese muffins combine perfectly spiced pumpkin muffins with cream cheese filling. Top the muffins with brown sugar crumb cake topping and you have an absolutely irresistible pumpkin spice breakfast treat.

stack of pumpkin cheesecake muffins

I originally published this recipe in 2013 and have since added new photos, a video tutorial, and more success tips.


It’s time to cross something off your fall to-do list: make cream cheese-stuffed pumpkin muffins!

Every year when the weather begins to cool down, I suddenly begin craving all of the season’s comforting flavors. I’m pretty sure I’m not alone hereโ€”a pumpkin-spice alarm goes off in all our brains. First, I prepare a batch of homemade pumpkin pie spice. And then one of the first recipes I prepare each year are these pumpkin cheesecake muffins.

One reader, Sam, commented: “I was looking for a Starbucks dupe and this wasn’t it… it was so much better! Moist, fluffy, and absolutely delicious… โ˜…โ˜…โ˜…โ˜…โ˜…”

Another reader, Isabel, commented: “Thank you, Sally, for yet another mouthwatering recipe! The house is still filled with the warm scent of pumpkin and spices from baking these pumpkin cream cheese muffins last night. They were the perfect way to welcome the arrival of fall, my favorite season. โ˜…โ˜…โ˜…โ˜…โ˜…”

Everything to Love About Pumpkin Cheesecake Muffins

plate of pumpkin cheesecake muffins

3 Parts to Pumpkin Cream Cheese Muffins

  1. Pumpkin Muffins: There’s many different ways to prepare pumpkin muffins. You could leave these muffins completely plain without the cream cheese filling and crumb cake topping and they’ll be similar to my regular pumpkin muffins. You could also try these pumpkin crumb cake muffins or mini cinnamon sugar pumpkin muffins instead.
  2. Cheesecake Filling: You need 4 simple ingredients for the cream cheese filling. Bring some brick cream cheese to room temperature, then beat it with 1 egg yolk, sugar, and a touch of vanilla extract. The egg yolk helps the cream cheese filling “set” like cheesecake.
  3. Crumb Topping: You also need 4 ingredients for the crumb topping including flour, melted butter, brown sugar, and cinnamon. Make the crumb topping first so it’s ready. It’s nearly the same crumb topping we use for peach muffins in the summertime.

You need 4 mixing bowls: 1 for the muffin’s dry ingredients, 1 for the muffin’s wet ingredients, 1 for the cheesecake filling, and 1 for the crumb cake topping.

2 images of batter for pumpkin cheesecake muffins
pumpkin cheesecake muffin batter in muffin pan
2 images of crumb cake topping in a bowl and sprinkled onto pumpkin cheesecake muffins

Overview: How to Make Pumpkin Cream Cheese Muffins

  1. Prepare crumb cake topping.
  2. Prepare pumpkin muffin batter. Use a whisk to bring all the ingredients together.
  3. Prepare cheesecake filling. You need a mixer for this step.
  4. Layer the pumpkin batter and cheesecake filling together.
  5. Add crumb cake topping. Press it down into the tops of each muffin so it sticks.
  6. Bake. Your kitchen will smell like a pumpkin spice candle!
pumpkin cheesecake muffins on a plate

Which part of these pumpkin cheesecake muffins will you like best? I’m not sure I can play favorites! There’s just so much to love because every layer has a different texture and taste. A moist and flavor-packed tender pumpkin muffin, generously spiced and lightly sweetened with brown sugar. The cheesecake is a tangy, yet sweet ripple of creamy goodness. And the buttery slightly crunchy crumbles on top add the perfect finishing touch.

Not to mention, they taste fantastic for breakfast with a cup of coffee and homemade pumpkin coffee creamer. Fall breakfast bliss!

pumpkin muffin filled with cream cheese and topped with crumb
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stack of pumpkin cheesecake muffins

Pumpkin Cream Cheese Muffins

5 Stars 4 Stars 3 Stars 2 Stars 1 Star 4.8 from 134 reviews
  • Author: Sally McKenney
  • Prep Time: 25 minutes
  • Cook Time: 22 minutes
  • Total Time: 50 minutes
  • Yield: 12-14 muffins
  • Category: Breakfast
  • Method: Baking
  • Cuisine: American
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Description

Like a delicious pumpkin roll, these pumpkin cream cheese muffins combine perfectly spiced pumpkin muffins with cream cheese filling. Top the muffins with brown sugar crumb cake topping and you have an absolutely irresistible pumpkin spice breakfast treat.


Ingredients

Crumb Topping

  • 1/3 cup (67g) packed light or dark brown sugar
  • 1 teaspoon ground cinnamon
  • 1/4 cup (4 Tbsp; 56g) unsalted butter, melted
  • 2/3 cup (84g) all-purpose flour

Pumpkin Muffins

  • 1 and 3/4 cups (219g) all-purpose flourย (spooned & leveled)
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • 1/2 teaspoon salt
  • 2 teaspoons ground cinnamon
  • 1 teaspoon store-bought or homemade pumpkin pie spice*
  • 1/2 cup (100g) packed light or dark brown sugar
  • 1/2 cup (100g) granulated sugar
  • 2 large eggs, at room temperature
  • 1 cup (227g) cannedย pumpkin puree
  • 1/2 cup (120ml) vegetable oil (or melted coconut oil)
  • 1/3 cup (80ml) milk
  • 1 teaspoon pure vanilla extract

Cream Cheese Filling

  • 6 ounces (170g) full-fat brick cream cheese, softened to room temperature
  • 1 egg yolk, at room temperature
  • 1/2 teaspoon pure vanilla extract
  • 3 Tablespoons (36g) granulated sugar

Instructions

  1. Preheat oven to 425ยฐF (218ยฐC). Spray a 12-count muffin pan with nonstick spray or line with cupcake liners. This recipe makes 12-14 muffins, so you may need a 2nd muffin pan or bake this recipe in batches.
  2. Make the crumb-topping first: Mix the brown sugar, cinnamon, and melted butter together in a small bowl until combined. Add the flour and use a fork to gently mix until crumbs form. Don’t over-mix into a paste. Just mix until it is crumbly. Set aside.
  3. Make the pumpkin batter: Whisk the flour, baking powder, baking soda, salt, cinnamon and pumpkin pie spice together in a large bowl. Set aside. In a medium bowl, whisk the brown sugar, granulated sugar, eggs, pumpkin, oil, milk, and vanilla extract together. Pour the wet ingredients into the dry ingredients and whisk or stir until just combined. Avoid over-mixing.
  4. Make the cheesecake filling: Using a handheld or stand mixer fitted with a paddle or whisk attachment, beat the cream cheese in a medium bowl on medium-high speed until smooth and creamy. Beat in the egg yolk, vanilla extract, and sugar until combined.
  5. Spoon 1 heaping Tablespoon of pumpkin muffin batter into the muffin cups. Layer with about 1 spoonful (not quite a full Tablespoon) of cheesecake filling, then another heaping Tablespoon of muffin batterโ€”or however much batter is needed to fill the cups all the way to the top. Some cheesecake filling may poke out of the top or on the sides. Sprinkle crumb topping onto each, then press it down into the tops of the muffins to help prevent it from falling off as the muffins bake.
  6. Bake for 5 minutes 425ยฐF (218ยฐC) then, keeping the muffins in the oven, reduce heat to 350ยฐF (177ยฐC)* and continue baking for another 15-17 minutes. The total time these muffins should be in the oven is around 20-22 minutes. Allow to cool for at least 10 minutes in the pan before serving.
  7. Cover leftover muffins tightly and store at room temperature for up to 2 days or in the refrigerator for up to 1 week.

Notes

  1. Freezing Instructions:ย For longer storage, freeze the muffins for up to 3 months. Thaw overnight in the refrigerator, then heat up in the microwave if desired.
  2. Special Tools (affiliate links):ย 12-count Muffin Pan | Cupcake Liners | Glass Mixing Bowls | Whisk | Electric Mixer (Handheld or Stand)
  3. Pumpkin Pie Spice:ย You can find pumpkin pie spice in the baking aisle of most grocery stores or make your own homemade pumpkin pie spice. If you donโ€™t have either and want to use individual spices, use 1/4 teaspoon each: ground ginger, ground nutmeg, ground cloves, and ground allspice. This is in addition to the 2 teaspoons of cinnamonโ€”you will still add that.
  4. Why the initial high oven temperature? Like I do for most muffin recipes, bake the muffins for 5 minutes at a very hot temperature. Then, keeping the muffins in the oven, switch to a lower temperature for the remaining bake time. This initial high temperature will quickly lift the muffin tops so they’re extra high, then the centers will bake during the lower temperature bake time. This trick makes beautiful bakery-style muffins every time.

sally mckenney headshot purple shirt.
About the Author

Sally McKenney

Sally McKenney is a baker, food photographer, and New York Times best-selling author. Her kitchen-tested recipes and step-by-step tutorials have given millions of readers the knowledge and confidence to bake from scratch. Sallyโ€™s work has been featured on TODAY, Good Morning America, Taste of Home, People, and more.

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Reader Comments and Reviews

  1. Betty says:
    September 24, 2026

    Is there any way to make these muffins without milk?

    Reply
    1. Trina @ Sally's Baking says:
      September 24, 2026

      Hi Betty, any kind of milk would work here (dairy free, etc) or even watered down heavy cream could work in a pinch!

      Reply