Pumpkin Cream Cheese Muffins have a layer of cheesecake nestled in a moist pumpkin muffin. Top with streusel for a fall breakfast so good you’ll be eating them all year.

It’s fall so we have to have a new pumpkin recipe, and you’re going to love these pumpkin cream cheese muffins. I tried to reproduce my favorite Chocolate Muffins that have a cheesecake filling, they’re my family’s all time favorite.
The challenge is getting the dollop of cream cheese filling to sink down into the muffins. For my chocolate cupcakes this works because the chocolate batter is pretty thin and the cheesecake filling has chocolate chips in it which weighs it down.
How was I going to thicken the cream cheese filing and still get a cheesecake type filling, I just used an egg yolk instead of the entire egg and then I tried adding it to the top. However, this is what I got which is not very pretty and is just a layer of cream cheese on top of a delicious pumpkin muffin. The streusel just clumped up.
Christy from The Girl Who Ate Everything has a recipe where she freezes cream cheese frosting and then puts it in the muffin. That’s just too much work for me for a breakfast muffin, and I wanted more of a cheesecake filling, so I settled for a layer of cheesecake and added streusel to the top.
These muffins are fabulous. Natalie was home and was my taste tester as we made batch after batch. The flavor of the muffin itself reminds you of fall with cinnamon, nutmeg and cloves in a muffin that’s not too sweet.
Can you use pumpkin pie spice
You can definitely substitute pumpkin pie spice in this recipe, just add 2 teaspoons and eliminate the cinnamon, nutmeg and cloves. I didn’t want the allspice and ginger that are generally in pumpkin pie spice, but if you love all those flavors, use it in these pumpkin muffins. If you make a lot of pumpkin recipes, then you might want to make your own pumpkin pie spice.
To account for the streusel topping, I decreased the sugar in the muffin, the topping not only adds sweetness but a great crunch. And did I mention how moist they are from the pumpkin itself. These are pretty amazing! There are a couple of steps but still start to finish it took less than 30 minutes to assemble.
How do you make Pumpkin Cream Cheese Muffins
Step 1: Make a streusel topping using your fingers to work the butter into flour, brown sugar and cinnamon.
Step 2: Combine the wet ingredients and the dry ingredients and add together until just combined.
Step 3: Beat cream cheese with an egg yolk, sugar and vanilla.
Step 4: Assemble by adding a layer of pumpkin, a layer of cream cheese, a layer of pumpkin and a final layer of streusel.
Step 5: Bake at 425º for 5 minutes and then reduce the oven to 350º and bake for 15 more minutes.
Why should you cook muffins at a high temperature
By starting the muffins out at a high temperature it gives them that bakery style lift, reducing it keeps them from burning before the centers are cooked. I use this technique for all my muffins.
FAQ’s and Tips
No, this recipe needs 100% pure pumpkin.
Too get tall muffins, start at 425º for 5 minutes and then reduce to 350º for 15 minutes.
Yes, substitute 2 teaspoons for the cinnamon, nutmeg and cloves.
Yes, it will only stay fresh for a couple of days in the refrigerator.
What should you do with the extra pumpkin
Most muffin recipes use 1 cup of pumpkin which will leave you ¾ of a cup if you have a 15 oz can. Since it’s not enough for a second batch, here are some ideas for what to do with the extra pumpkin.
- You could make Pumpkin Cheese Cake Balls, it only takes ½ cup of pumpkin
- For Pumpkin Snickerdoodles you need ¾ cup of pumpkin
- Go savory and make Apple Cider Chili which calls for ½ cup of pumpkin
- Give it to your dog, it helps with diarrhea or upset stomachs
More FALL recipes
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Pumpkin Cream Cheese Muffins
Ingredients
STRESUEL
- ¼ cup brown sugar
- ½ cup flour
- 1 teaspoon cinnamon
- 4 tablespoons butter cold cut into pieces
- ⅛ teaspoon salt
MUFFINS
- 1 ½ cups flour
- 1 ½ teaspoons cinnamon
- ⅛ teaspoon cloves
- ¼ teaspoon nutmeg
- 1 teaspoon baking soda
- 1 teaspoon baking powder
- ½ teaspoon salt
- ⅔ cup brown sugar
- ½ cup oil
- ¼ cup buttermilk
- 1 teaspoon vanilla
- 1 cup pumpkin puree
- 2 eggs
FILLING
- 8 ounces cream cheese room temp
- ⅓ cup sugar
- 1 teaspoon vanilla
- 1 egg yolk
Instructions
- Preheat oven to 425º. Line 14 muffin tins with liners
STREUSEL
- In a small bowl, combine the brown sugar, flour, cinnamon, and salt. Add cold butter and using fingers combine.
MUFFINS
- Whisk together the flour, cinnamon, cloves, nutmeg, baking soda, baking powder and salt. In a separate bowl, combine the brown sugar, oil, buttermilk, vanilla, pumpkin and eggs. Whisk until well combined. Add pumpkin mixture to dry mixture and stir, just until combined.
FiILLING
- In a small bowl, combine all ingredients and mix with a hand mixer until smooth.
- To assemble, place about 2 tablespoons of pumpkin mixture in the muffin tin, add about 1 tablespoon cream cheese and then add another 2 tablespoons of pumpkin mixture so that the batter reaches the top of the tin. Cover with streusel and press into the batter.
- Bake for 5 minutes at 425º, then reduce oven to 350º, (don’t remove the muffinbake an additional 15 minutes for a total of 20 minutes. A toothpick inserted in the center should come out clean. Let cool in the pan for about 10 minutes before removing.
Notes
Recipe Tips
- You can substitute 2 teaspoons of pumpkin pie spice and leave out the cinnamon, cloves and nutmeg.
- To get tall muffins, start at 425º for 5 minutes and reduce temperature without opening the door to 350º for 15 minutes.
- You can freeze the leftover pumpkin.
Nutrition
If you make Pumpkin Cream Cheese Muffins, be sure to leave a comment and/or give this recipe a rating! Above all, I love to hear from you guys and always do my best to respond to each and every comment. And of course, if you do make this recipe, don’t forget to also tag me on Instagram! I would love to see your creation.