Pumpkin Cheesecake Muffins

close up of pumpkin cheesecake muffin

It’s a difficult thing to admit, but: Jay doesn’t have a sweet tooth. He didn’t even eat fruit when I first moved in, several years ago, and would turn his nose up at sugary vegetables, such as sweet potatoes and winter squash. While creamy custards and ice cream make me weak in the knees, he can take or leave them, passing them up any day for a bag of salty chips or a plate of greasy french fries.

Every so often, though, I catch a gleam of enthusiasm for some childhood classic: pumpkin pie, butterscotch ice cream, tapioca pudding, the old standbys we all enjoy as children. During a muffin phase a few years back, Jay spoke lovingly of pumpkin cheesecake ones he used to get from Rebecca’s Mighty Muffins in Santa Cruz during his college days. I looked around for recipes, but didn’t find anything that seemed quite right. I wanted a sturdy, not-too-sweet muffin made with butter rather than vegetable oil, redolent with the flavors of brown sugar and warming spices. I wanted a smooth, creamy filling with the salty tang of cheesecake, and plenty of it, so that you got some in each bite. Quite pleased with the results, Jay even set aside the chips to devour a few.
The first real rain of the season has brought on a desperation to bake with winter squash, so I decided to make these muffins, but I made a few changes from my original recipe, browning the butter, adding freshly grated ginger to the cheesecake mixture and toasted pecans to the muffin batter. They are delicious, but, I don’t know, I kind of prefer the plain-Jane originals. So here’s the original recipe, with the ginger-pecan variation at the end.

shot of baked pumpkin half

You can use any dense fleshed winter squash for this recipe. I actually don’t favor pumpkins for baking, as they tend to be stringy, watery and bland. This time, I used an incredibly dense-fleshed red kuri squash, but kabochas, hokkaidos and butternuts are other excellent choices. If your squash puree is watery, or if you use canned pumpkin (which is fine), drain it for about 3o minutes in a fine mesh sieve, lined with cheesecloth if necessary.
For the squash puree, preheat the oven to 375º. Lightly oil a rimmed baking sheet. Using a large, sharp chef’s knife, cut the squash in half lengthwise. Leaving the seeds in (they are much easier to scrape out once the squash is cooked, and also add flavor and moisture to it during baking) place the squash cut side down on the baking sheet. Roast in the oven until tender when poked with a knife. Let cool. Scrape out the seeds and discard, and scoop the flesh out of the skin. Puree in a food processor or food mill until smooth.

For more pumpkin recipes:

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Pumpkin Cheesecake Muffins

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These filled muffins are perfect for fall!
Prep: 20 minutes
Cook: 30 minutes
Total: 50 minutes
Servings: 12 muffins


For the cheesecake filling:

  • 6 oz. cream cheese, at room temperature
  • 1/4 cup sugar
  • 1 egg yolk
  • 1 tablespoon sour cream or plain yogurt
  • 1 tablespoon lemon juice
  • 1/2 teaspoon vanilla
  • pinch salt

Pumpkin Muffins:

  • 1 stick unsalted butter, melted and cooled slightly (4 oz.)
  • 3/4 cup squash puree, or canned pumpkin
  • 1/4 cup buttermilk
  • 3/4 cup packed brown or unrefined sugar
  • 2 tablespoons molasses
  • 2 eggs
  • 2 cups flour (I use equal parts whole and white spelt)
  • 1 1/2 teaspoons baking powder
  • 1/4 teaspoon baking soda
  • 1/2 teaspoon salt
  • 1 teaspoon cinnamon
  • 1/2 teaspoon ginger
  • 1/4 teaspoon allspice
  • 1/8 teaspoon freshly grated nutmeg


For the cheesecake filling:

  • Beat the cream cheese and sugar together until smooth. Add yolk, sour cream, lemon juice, vanilla and salt to combine throughly. Put in fridge while you get on with the muffins.

Pumpkin Muffins:

  • Preheat the oven to 350º. Line a standard 12-cup muffin pan with muffin liners (does that sound a bit dirty, or is it just me?)
  • In a medium bowl, whisk together the melted butter, squash puree, buttermilk, sugar, molasses and eggs to combine.
  • In a large bowl, sift together the dry ingredients. Make a well, and gently fold in the wets until just combined. Divide the batter evenly between the cups.
  • Now comes the fun part, and there are two possible ways to go about it. You can either use the back of a spoon to make a small well in the center of each muffin, and spoon the cheesecake filling in. Or use a piping bag fitted with a smallish, plain tip (or a plastic baggie which you will snip the corner off of) and fill with the cream cheese mixture. Plunge the tip into the center of the muffin, and gently squeeze out a couple tablespoons. The muffin will puff up. Repeat with the remaining muffins until you have used up all the filling.
  • Bake the muffins on the center rack until puffed and golden, about 30 minutes.


Brown-butter pecan pumpkin muffins with ginger cheesecake filling.  Follow the above directions, making the following changes:
Add 1-2 teaspoons finely grated fresh ginger to the cheesecake filling. For the muffins, brown the butter by cooking it over medium heat, swirling occasionally, until it browns, smells nutty and makes you swoon with olfactory pleasure. Let cool to warm.
For the spices, substitute the following, omitting the allspice:  1 teaspoon ground ginger, 1/2 teaspoon cinnamon, 1/4 teaspoon freshly grated nutmeg.
Toast 3/4 pecans, let cool, and chop coarsely. Gently fold in after combining the wets and dries.
Nutritional values are based on one muffin.


Calories: 297kcal | Carbohydrates: 38g | Protein: 4g | Fat: 14g | Saturated Fat: 8g | Cholesterol: 80mg | Sodium: 192mg | Potassium: 207mg | Fiber: 1g | Sugar: 21g | Vitamin A: 2885IU | Vitamin C: 1.2mg | Calcium: 78mg | Iron: 1.7mg
Making this? I'd love to see!Tag your snaps @The_Bojon_Gourmet and #bojongourmet!

top down shot of pumpkin cheesecake muffins on a wire rack

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One thought on “Pumpkin Cheesecake Muffins”

  1. It sounds like Jay is on his own ketogenic diet: low carbs and plenty of fats. This recipe seems like the perfect thing for a day off of the regular meal plans. I’ll hang on to my muffin tin just for this treat.