Fall is in the air! These pumpkin cheesecake muffins made with fresh milled flour are a cozy treat to enjoy on a cool crisp fall day. Enjoy warm or chilled with your favorite fall drink!

What You’ll Need To Make These Pumpkin Cheesecake Muffins Made With Fresh Milled Flour
Muffins
Fresh Milled Soft White Flour
Baking Powder
Baking Soda
Cinnamon
Pumpkin Pie Spice
Salt
Eggs
Pumpkin Puree
Sugar
Brown Sugar
Butter
Milk
Vanilla Extract
Cheesecake Filling
Cream Cheese
Sugar
Egg
Vanilla Extract
Streusal Topping
Fresh Milled Soft White Wheat Flour
Butter
Brown Sugar
Cinnamon







How To Make Your Own Pumpkin Pie Spice
If you don’t have pumpkin pie spice you can make your own in just a few minutes!
- 3 tablespoons ground cinnamon
- 2 teaspoons ground ginger
- 1 1/2 teaspoon ground cloves
- 2 teaspoon ground nutmeg
- 1 1/2 teaspoons ground allspice
Whisk together and store in a spice container or small mason jar.
How To Store These Pumpkin Cheesecake Muffins
Let the muffins cool completely and store in an airtight container in the fridge for 5-7 days.
Can I Freeze Pumpkin Cheesecake Muffins?
Yes! Cool them completely and place in a freezer bag or container for up to 3 months. Let them thaw at room temperature and enjoy!
Other Recipe Variation Ideas
- Use jumbo muffin tins and liners for a bakery style muffin. *Baking time may need to be slightly increased for this.
- Add mix-ins like chocolate chips or nuts to your batter before baking.
- If you prefer a plain pumpkin muffin just leave out the streusel topping and cheesecake filling.
- Enjoy with a simple glaze drizzled over the top. (1 cup powdered sugar, 2-4 tablespoons milk, 1/4 tsp vanilla extract mixed until smooth. Use less milk for a thicker glaze and more for a thinner glaze.)
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Pumpkin Cheesecake Muffins Made With Fresh Milled Flour
Ingredients
Method
- Spray or line your cupcake pans with cupcake liners. Set aside.
- Make the streusel topping by mixing the flour, brown sugar, and cinnamon together with a fork until combined. Then add the melted butter and stir until just combined. Set aside.It will set up a little more as it cools and you can break it up with your fork before adding to the muffins.
- Next, make the cheesecake filling by adding your softened cream cheese, sugar, egg, and vanilla extract to a small mixing bowl. Then using a hand mixer or stand mixer beat until smooth and creamy. Set aside.
- Preheat the oven to 425F.
- In a mixing bowl combine flour, baking powder, baking soda, cinnamon, pumpkin pie spice, and salt. Whisk until combined.
- In a separate mixing bowl add pumpkin, eggs, sugar, brown sugar, melted butter, milk and vanilla extract. Mix until combined.
- Add your dry ingredients to the wet ingredients and mix until combined. Be careful to not overmix.
- Spoon 3 tablespoons of muffin batter into muffin cups. Then add 1 tablespoon of cheesecake filling. You can either gently spread the cheesecake into an even layer or use a butter knife to swirl it. Finish by adding 2 tablespoons of muffin batter on top of the cheesecake layer.
- If using the streusel topping, sprinkle about 1 tablespoon of topping on each muffin and gently press it in so it doesn't fall off when baking.
- Bake for 5 minutes at 425F and then reduce the heat to 350F and finish baking for about 15 minutes.
- Cool in the pan for 5-7 minutes and then remove and finish cooling on a cooling rack.
- Store completely cooled muffins in an airtight container in the fridge for up to a week.












These smell and look amazing. Can’t wait for them to cool down and take a bite!
Enjoy!
I used a cup of mini chocolate chips instead of the cream cheese filling and streusel topping. They turned out great! Made enough for 16 nice sized muffins. I’m just getting into using freshly milled flour and will make these again.
Good addition!