You’ll find a hidden layer of cheesecake inside these incredibly moist pumpkin cream cheese muffins. Topped with streusel for a fall breakfast you can enjoy all year round.
Wait until you bite into one of these, your morning just got so much better!

It’s fall so we have to have a new pumpkin recipe, and you’re going to love these scrumptious pumpkin cream cheese muffins. My goal was to reproduce my favorite Chocolate cream cheese cupcakes that have a cheesecake filling, they’re my family’s all time favorite, but more of a dessert than a breakfast muffin.
The challenge was 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.
Getting the cream cheese filling thick enough was the trick. I used an egg yolk instead of the entire egg which helped but and when I added it to the top, this is what I got. Not very pretty and it was just a layer of cream cheese on top of a delicious pumpkin spice 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. Instead, I added a layer of cheesecake between two pumpkin layers and topped the whole thing with the streusel from my blueberry muffins.
Voilà, pumpkin muffins with a cream cheese filling. A light moist pumpkin muffin with a surprise bite of cheesecake filling. 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.
If you love that fall pumpkin flavor, try making pumpkin apple bread for a moist quick bread that you can prep in about 15 minutes. If pumpkin’s not your thing, go with a pear muffin or mixed berry muffins that use frozen berries.
Why cream cheese muffins are the best♥️
- You can make them ahead of time and they won’t dry out.
- Did someone say cheesecake!
- Beautiful muffins that also taste great.
- A breakfast 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 found in pumpkin pie spice, but if you love all those flavors, use it in these pumpkin streusel muffins. If you find yourself making 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.
Ingredients to make pumpkin muffins
- Canned pumpkin – you won’t use an entire can, just one cup. Make sure you get pumpkin puree not pumpkin pie filling.
- Buttermilk – if you don’t have any, you can make your own by adding a tablespoon of lemon juice to a cup of milk,
- Vegetable oil – as much as I like butter, oil works better in muffins.
- Eggs – you need two for the batter and an egg yolk for the cream cheese filling.
- Dry goods – flour, sugar, brown sugar, baking soda and baking powder.
- Pantry items – cinnamon, cloves, nutmeg, vanilla and butter.
How do you make pumpkin streusel muffins
Step 1: Make a streusel topping using your fingers to work the butter into the 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. These need to cool completely before eating so that the cream cheese filling has a chance to set.
Due to the filling, you’ll need to refrigerate once cool. I prefer a cream cheese filled muffin a little cool or at room temperature. If you want a warm muffin, go with an apple cider muffin.
This is a perfect muffin recipe for make ahead occasions. Between the pumpkin and the cream cheese, they’ll stay fresh and moist for several days. You can also freeze them and let them come to room temperature before serving.
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.
FAQs and Tips
You can not use pumpkin pie filling, this recipe needs 100% pure pumpkin.
Too get tall muffins, start at 425º for 5 minutes and then reduce to 350º for 15 minutes. Gives you beautiful tall muffins everytime.
You can substitute pumpkin pie spice in pumpkin muffins. Use 2 teaspoons instead of the cinnamon, nutmeg and cloves.
You can freeze canned pumpkin for future recipes, it will only stay fresh for a couple of days in the refrigerator.
What can you do with extra pumpkin
Most muffin recipes use 1 cup of pumpkin which will leave you with 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
- You can freeze it
What can you serve with pumpkin muffins
More Fall recipes you’ll love
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Pumpkin Cream Cheese Muffins
Ingredients
STREUSEL
- 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
Equipment
- Muffin tin
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.
Video
Barbara’s Tips + Notes
- You can freeze leftover pumpkin for future use.
- You can substitute 2 teaspoons of pumpkin pie spice and leave out the cinnamon, cloves and nutmeg.
- These muffins are best served at room temperature or slightly cool.
- To freeze the muffins, let them cool completely and freeze. Let them warm up to room temperature before serving.
These look so delicious! Perfect for the fall and breakfasts!
The streusel topping puts these beyond delicious!