This post may contain affiliate links. If you make a purchase through links on our site, we may earn a commission. Please read our disclosure policy.
Why I Love These Muffins
Baking from scratch may seem like a lot of work. Not only do you have to make sure you have all the ingredients, but you also need time to mix them together. That said, you have to admit that when you bite into a warm, fresh-from-the-oven homemade baked good, you are in heaven. These pumpkin cheesecake muffins check every box for me. They’re soft and spiced like a good pumpkin bread, but then there’s that creamy cheesecake center and a streusel on top that makes them feel just a little extra special.
I love that when you bake your own goods at home, you can taste the quality ingredients that make up each bite, and you’re cognizant of the time and love that was put into each treat. I know baking doesn’t relax everyone as it does for me, but I also know everyone enjoys something delicious. These pumpkin cheesecake muffins are totally worth the effort, which, in all honesty, isn’t really too much.
Here’s why you’ll want to make them:
- Three irresistible layers – spiced pumpkin muffin, creamy cheesecake, and crunchy oat streusel.
- No mixer needed – just bowls and whisks!
- Perfect for any time – enjoy at breakfast, as a snack, or for dessert (trust me, they never last long).
- A make-ahead treat – they’re freezer-friendly and may even taste better the next day!
Pumpkin Cheesecake Muffin Ingredients
These pumpkin cheesecake muffins use simple ingredients for a delicious treat:
- Whole wheat flour – Adds a nutty texture that holds up during baking.
- All-purpose flour – The more traditional flour commonly used, which forms the base structure of the muffins.
- Rolled oats – Add some heft and crunch to the streusel topping.
- Brown sugar and granulated sugar – Two types of sugar to sweeten both the streusel and muffins.
- Pepitas – Add a seasonal crunch along with some color.
- Ground cinnamon, ground ginger, and nutmeg – All give that warm fall flavor you’re looking for.
- Unsalted butter – Helps the streusel form crisp, golden clumps.
- Cream cheese – Creates the creamy, tangy cheesecake center.
- Egg – Used in both the cheesecake mixture and muffin batter for structure.
- Vanilla extract – A bit of extra flavor. It’s always economical to make your own vanilla extract at home.
- Pumpkin puree – Brings moisture and rich pumpkin flavor to the muffin.
- Neutral oil – Helps to keep the muffins moist and tender.
- Molasses – Deepens the flavor with autumn warmth.
- Baking powder – Helps the muffins rise.
- Baking soda – Balances acidity and gives lift.
- Kosher salt – Enhances all the flavors and balances the sweetness.
The full amount of each ingredient can be found in the recipe card below.
How to Make Pumpkin Cheesecake Muffins
These pumpkin cheesecake muffins can be made in 5 steps:
Step 1: Prepare the streusel – In a bowl, combine whole wheat flour, oats, brown sugar, pepitas, and cinnamon. Cut in cold butter and work into the mixture until it looks like wet sand. Place the streusel in the freezer to chill while preparing the remaining ingredients.
Step 2: Make the cheesecake filling – In a separate bowl, whisk together cream cheese, sugar, and egg until smooth. Set aside.
Step 3: Create the muffin batter – In a large bowl, whisk the pumpkin puree and brown sugar until smooth. Add in the eggs, oil, molasses, and vanilla extract, and whisk until smooth. Add in the all-purpose flour, whole wheat flour, baking powder, baking soda, cinnamon, ginger, nutmeg, and salt. Whisk until no dry streaks remain.
Step 4: Prepare the muffins – Spray a 12-cup muffin tin with nonstick spray or line with paper cups. Add the cheesecake batter to the pumpkin muffin batter. Swirl together slightly without fully combining. Spoon into each muffin tin.
Step 5: Bake – Pile on the streusel topping to each muffin. Bake in a preheated 350°F oven for 20-25 minutes until the tops are set and slightly firm to the touch. Let cool in the pan for 15 minutes, then transfer to a cooling rack.
Recipe Tips
- Use room-temperature cream cheese – It blends more smoothly and makes the filling super silky.
- Don’t overmix the batter – Stir just until you don’t see dry flour streaks to keep the muffins soft.
- Freeze your streusel – Cold streusel holds its shape better during baking.
- Muffin liners are optional – These muffins bake up soft and moist, and liners can make cleanup easy. Plus, if you’re serving these, a liner can feel easier to handle. Personally, I tend to grease the muffin tins well and avoid using liners.
- Let them cool (a bit) – The filling sets up as they cool, but they’re still delicious slightly warm.
Follow These Tips
Serving & Storage
Serve these muffins slightly warm or at room temperature. They can be enjoyed with coffee or tea in the morning, as a midday snack, or as a dessert after dinner. Since the recipe makes 12 servings, they’re perfect for serving a crowd!
Store in an airtight container in the fridge for up to 5 days. Allow to come to room temperature or warm slightly before serving. If desired, warm muffins in the microwave for 15-20 seconds or in a 300°F oven for 5-8 minutes for a fresh-baked texture. Each muffin can also be individually wrapped and frozen or placed in a freezer-safe container for up to 2 months. Thaw overnight in the fridge before enjoying.
More Pumpkin Desserts
Have I Convinced You to Make This Recipe?
I hope you make this recipe and put some food on your table. Leave a comment and share a star rating so you can let others know how much you love this recipe. This helps show others that this is a recipe they, too, can make, enjoy, and love!
Pumpkin Cheesecake Muffins
Ingredients
For the streusel topping
- ⅓ cup whole wheat flour
- ⅓ cup rolled oats
- ⅓ cup light brown sugar
- ⅓ cup roasted pepitas (pumpkin seeds) or nut of choice, chopped
- 1 tsp ground cinnamon
- 5 tbsp unsalted butter
For the cheesecake filling
- 6 oz cream cheese room temperature
- ⅓ cup granulated sugar
- 1 large egg
For the pumpkin muffins
- 1 cup pumpkin puree
- ½ cup light brown sugar
- ⅓ cup neutral oil
- 2 large eggs
- 2 tbsp molasses
- 1 tsp vanilla extract
- 1 cup all-purpose flour
- ½ cup whole wheat flour
- 1 tsp baking powder
- ½ tsp baking soda
- 1 tsp ground cinnamon
- 1 tsp ground ginger
- ¼ tsp ground nutmeg
- 1 tsp kosher salt
Instructions
- Preheat oven to 350°F.
- Prepare the streusel topping: In a medium bowl, combine the whole wheat flour, oats, brown sugar, roasted pepitas, and cinnamon. Stir to evenly combine. Cut butter into small pieces and work it into the mixture until it looks like wet sand, as would be done for pastry dough. Place in the freezer until ready to assemble the muffins.⅓ cup whole wheat flour, ⅓ cup rolled oats, ⅓ cup light brown sugar, ⅓ cup roasted pepitas (pumpkin seeds) or nut of choice, chopped, 1 tsp ground cinnamon, 5 tbsp unsalted butter
- Prepare the cheesecake filling: In a small bowl, whisk the cream cheese, granulated sugar, and egg until smooth with no lumps.6 oz cream cheese, ⅓ cup granulated sugar, 1 large egg
- Prepare the muffin batter in a large bowl: Whisk the pumpkin puree and brown sugar until smooth. Whisk in the eggs, oil, molasses, and vanilla extract until combined. Add the all-purpose flour, whole wheat flour, baking powder, baking soda, cinnamon, ginger, nutmeg, and salt. Whisk until just combined and no streaks of flour remain.1 cup pumpkin puree, ½ cup light brown sugar, ⅓ cup neutral oil, 2 large eggs, 2 tbsp molasses, 1 tsp vanilla extract, 1 cup all-purpose flour, ½ cup whole wheat flour, 1 tsp baking powder, ½ tsp baking soda, 1 tsp ground cinnamon, 1 tsp ground ginger, ¼ tsp ground nutmeg, 1 tsp kosher salt
- Assemble the muffins: Spray a 12-cup muffin tin with nonstick baking spray. Pour the prepared cheesecake batter into the muffin batter. Fold together sparingly until the mixture looks just swirled. Using a half-cup ice cream scoop, divide batter among the prepared muffin tins. Top with the prepared streusel.
- Bake in the preheated 350°F oven until puffed and set, 20-25 minutes. A toothpick inserted into the batter portion of the muffin should come out mostly clean. Once baked, remove from the oven and cool for 15 minutes on a cooling rack.
Video
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
Did you make this? Leave a comment below!
Styling: Addelyn Evans | Photography: Dera Burreson
Made these but poured the cheesecake mixture into the pumpkin batter in the cupcake tin. Then circular swirled with a bamboo scewer a couple of times.
To serve: I made a caramel sauce to drizzle on top of the muffin with a small scoop of vanilla caramel chocolate swirl ice cream.
Next day I had a muffin slightly warmed in the toaster oven. Cut in half and put a small pat of real butter on it. Delicious with my morning coffee on a chilly day.
Love this recipe!
love your recipes! you remind of when i grew up cooking and baking with my great aunt. good memories cooking with family.
Just made these muffins now. Smell delicious. There is a lot of batter so muffins are filled to the brim. There is quite a bit more streusel topping than is needed.
I find it takes at least 33 minutes to bake like someone else has mentioned. Can hardly wait to taste them.
I am from Port Hood, Cape Breton in Canada and have just made your pumpkin cheesecake muffins. They are delicious. My new favorite muffin. Thank you for sharing your recipes. I will definitely make these again.
I made this outstanding recipe today. Our family loved them! Thanks for sharing it.
I bake for a little assisted living memory care home and will definitely make these in the very near future. I can tell this is going to be a five-star wonder.
I just have to ask wherever did you find such a cute cooling rack?