These easy Pumpkin Cheesecake Muffins are flavored with pumpkin pie spice and puree, layered with a sweet cream cheese filling, and topped with cinnamon streusel. They are moist and fluffy - the perfect Autumn muffin!
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My pumpkin coffee cake is a fall recipe favorite and these muffins taste as if mini versions of it have been drizzled with cream cheese icing! They're soft and moist thanks to the kefir, vegetable oil, and pumpkin puree.
If you've perused through all of my recipes, you may have noticed that I love baking with Lifeway Kefir! They sponsored this tasty muffin recipe and are also based around Chicago! Their mission is inspiring and their kefir adds probiotics and nutrients to many of my recipes, including these muffins.
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Why You'll Love This Recipe
- These pumpkin cream cheese muffins are like my delicious pumpkin pie cheesecake bars in muffin form!
- The cream cheese filling is less dense than traditional cheesecake which works perfectly with the fluffy muffins.
- The cinnamon streusel topping is the same as in my coffee cake muffins. It adds an extra sweet, spiced crunch to these cream cheese muffins.
- Enjoy Starbucks pumpkin muffins at home! Even though this recipe has 3 components, they are all surprisingly easy to make in less than an hour.
Recipe Ingredients
You'll need the following ingredients to make these delicious Pumpkin Cream Cheese Muffins:
Ingredient Notes:
- Pumpkin pie spice gives these muffins their classic fall flavor. Use a store-bought blend from your grocery store's spice aisle, or make your own by combining cinnamon, nutmeg, ginger, allspice, and cloves!
- Pumpkin puree is the star of this recipe! Be sure to use 100% pumpkin and not pumpkin pie filling. No need to blot it dry, either. Libby's Pure Pumpkin is my go-to, but any brand should work!
- Vegetable oil adds moisture to these muffins. You can use vegetable, canola, or any other neutral oil.
- Lifeway Organic Plain Whole Milk Kefir adds tang and helps lighten up the cheesecake filling.
- Cream cheese gives the filling traditional cheesecake flavor. I recommend using full-fat cream cheese and make sure it softens completely at room temperature ahead of time to avoid clumps in your filling.
See recipe card below for a full list of ingredients and measurements.
Substitutions & Variations
- For a simple pumpkin spice muffin, skip the streusel topping and/or cream cheese filling.
- Make these into jumbo bakery style muffins by using a jumbo muffin tin (you may need to adjust the bake time), or try my pumpkin donuts drizzled with cream cheese icing!
- For an even more decadent version, drizzle the tops of the muffins with a cream cheese glaze.
- Mix your favorites, like chopped nuts or cinnamon chips, into the pumpkin muffin batter before baking.
- If you can't get your hands on Lifeway kefir, you're welcome to substitute with an equal amount of buttermilk.
This recipe has not been tested with other substitutions or variations. If you replace or add any ingredients, please let us know how it turned out in the comments below!
How to Make Pumpkin Cheesecake Muffins
Step 1: In a large bowl, mix the softened cream cheese, granulated sugar, and kefir until smooth and no lumps remain. Set aside.
Step 2: To make the streusel, combine the flour, brown sugar, cinnamon, and melted butter until there are no dry pockets of flour. Set aside.
Step 3: For the muffin batter, whisk together the flour, baking powder, baking soda, salt, cinnamon, and pumpkin pie spice.
Step 4: In a separate bowl, mix the vegetable oil, granulated and brown sugar, eggs, vanilla extract, kefir, and pumpkin puree to combine.
Step 5: Fold the dry ingredients into the wet ingredients until just combined.
Step 6: Fill muffin liners ¼ full, then top with a small scoop of the cream cheese mixture.
Step 7: Top off with muffin batter until ⅔ to ¾ full, then swirl on more of the cream cheese mixture. Top them off with a sprinkle of streusel.
Step 8: Bake at 425°F for 5 minutes, then reduce the temperature to 350°F and bake until a toothpick comes out clean.
Expert Baking Tips
- Use a scale to measure the dry ingredients and weigh in grams as written in the recipe card below (see "metric" tab).
- Don't overmix the batter to ensure the muffins turn out moist and fluffy.
- For easier and cleaner batter distribution, use a cookie scoop!
- Don't skip starting the muffins at a higher oven temperature! This helps the muffins rise and create taller muffin tops.
Common Questions
No, be sure to use 100% pure pumpkin. Pumpkin pie filling contains added sugar, spices, and sometimes additional preservatives or chemicals.
Pumpkin pie spice is usually made with cinnamon, nutmeg, ginger, allspice, and cloves. For specific measurements, try this pumpkin pie spice recipe.
Lifeway Kefir can be found at lifewaykefir.com or in the dairy section of many grocery and convenience stores across the U.S.
Storage
Room Temperature
These pumpkin cheesecake muffins are best enjoyed within a day so that the crumb topping is still crunchy. However, they can be stored in an airtight container at room temperature for up to 4 days.
Freezing Instructions
Feel free to store these muffins in a freezer-safe container for up to 1 month. Let them thaw at room temperature before enjoying!
More Pumpkin Recipes You'll Love
Did you try this recipe?
Let us know what you thought by leaving a comment below and sharing it on Instagram, Facebook, & Pinterest!
Thank you!
-Kayla
📖 Recipe
Easy Pumpkin Cheesecake Muffins with Streusel
Equipment
- Mixing bowls
- Measuring spoons
- Whisk
- Spatula
- Muffin pan(s) with liners
Ingredients
Cream Cheese Filling
- 6 ounces (170.1 g) cream cheese room temperature
- ¼ cup (50 g) granulated sugar
- 1 tablespoon Lifeway Plain Organic Whole Milk Kefir room temperature
Cinnamon Streusel Topping
- 4 tablespoons (56 g) unsalted butter measured then melted
- ⅔ cup (83.33 g) all-purpose flour weighed in grams or spooned and leveled
- ½ cup (100 g) brown sugar light or dark, packed
- 1 teaspoon ground cinnamon
Pumpkin Muffins
- 2 cups (250 g) all-purpose flour weighed in grams (see metric tab) or spooned and leveled
- 1 teaspoon baking soda
- 1 teaspoon baking powder
- ¾ teaspoon salt
- 1 teaspoon ground cinnamon
- 1½ teaspoons pumpkin pie spice
- ½ cup (120 g) vegetable oil
- ½ cup (100 g) granulated sugar
- ½ cup (100 g) brown sugar light or dark, packed
- 2 large eggs room temperature
- 1½ teaspoons vanilla extract
- ¼ cup (60 g) Lifeway Plain Organic Whole Milk Kefir room temperature
- 1 cup (245 g) pumpkin puree
Instructions
- Preheat oven to 425°F and fill a muffin pan with liners (or grease with nonstick spray).
Cream Cheese Filling
- In a small bowl, mix together the softened cream cheese, sugar, and kefir until smooth.
Cinnamon Streusel Topping
- In a medium bowl, whisk together the flour, brown sugar, and cinnamon. Mix in the melted butter until completely combined.
Pumpkin Muffins
- In a medium bowl, whisk together the flour, baking soda, baking powder, salt, cinnamon, and pumpkin pie spice.
- In a large bowl, whisk together the vegetable oil, sugars, eggs, vanilla extract, kefir, and pumpkin puree until combined well.
- Fold the dry ingredients into the wet ones with a spatula just until the flour streaks disappear.
- Fill muffin liners ¼ full with pumpkin batter. Add about 1 tablespoon of cream cheese filling on top, and then fill to ⅔ - ¾ full with muffin batter. Top with the remaining cream cheese filling and then sprinkle cinnamon streusel on top.
- Bake on the middle rack at 425°F for 5 minutes, then reduce to 350°F without opening the oven door. Continue baking until a toothpick comes out clean (about 15-20 more minutes; 20-25 minutes total).
- Let the muffins cool in the pan for about 10 minutes, then transfer to a cooling rack.
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Daisy Hernandez says
this is an awesome recipe! i used 2% milk instead of kefir because they were out at the store i was at and they still came out delicious 😋!
Kayla Burton says
I'm so glad they worked well with 2%! Thank you for sharing!! 🙂
Angela says
Made this for the first time yesterday and it’s delicious! Got rave reviews at our team meeting. Will make again!
Kayla Burton says
Amazing!! Thanks, Angela! <3
Liv Hunt says
This recipe was amazing I ran out of the cream cheese part while assembling the muffins but other than that they were very good.
Patricia Martinescu says
The most delicious, moist cream cheese pumpkin muffins! Perfect for meal prep. Better than Starbucks. By far!
Georgiann says
Can I use whole milk in place of the kefir?
Kayla Burton says
I'd recommend buttermilk as a substitute but if you can't get your hands on that either, whole milk should be okay! I'd love to hear how it works if you try it 🙂