Pumpkin Cheesecake Muffins are a bakery-style treat made with spiced pumpkin muffin batter, a sweet cream cheese topping and plenty of chocolate chips. These moist, flavorful muffins are simple to make at home and taste just like the Starbucks favorite for a fraction of the cost.
I cannot believe how easy these were. My kids already asked if we can make them again tomorrow.
- Megan T.
Jump to:
Bailey's Thoughts ...
When I tell you these are my kids' favorite thing I bake, I mean it. Pumpkin cheesecake muffins beat out birthday cakes, cookies, even cinnamon rolls. I already know that when they come home from college or walk through the door with their own kids one day, these muffins will be waiting. It's the recipe that says, "You're home."
Spiced pumpkin batter stays soft and tender, the tangy cream cheese bakes into a silky swirl, and the chocolate chips melt just enough to streak through the crumb. They look bakery-fancy, but the process is simple: two bowls, a quick whisk, and a swirl of topping before the oven does the rest.
For best results, let your cream cheese come to room temperature (no shortcuts here - it makes all the difference). Gently fold the batter instead of beating it into submission, and don't forget to scatter a few chocolate chips on top for those bakery-style muffin caps that make them look store-bought in the best way.
-Bailey
P.S. If you love these, you should absolutely try my pumpkin mini muffins. Same cozy energy, just bite-sized!
Ingredients + Substitutions
All-purpose flour: Provides structure to the muffins. Substitutions: Up to 50% of the all purpose flour can be white whole wheat (full swap makes muffins dense).
Baking powder: Lifts the muffins so they stay tall.
Baking soda: Helps with browning and lift.
Pumpkin pie spice: Warm spice blend for classic pumpkin flavor. Substitution: Use 1 ½ teaspoons cinnamon + ½ teaspoon ginger + ¼ teaspoon nutmeg in place of 2 ¼ teaspoons pumpkin pie spice.
Granulated sugar: Sweetens and helps the crumb stay moist. Substitution: Light brown sugar 1:1 (muffins will be slightly darker and richer).
Vegetable oil: Keeps the crumb soft and moist. Substitution: Neutral oil like canola or grape seed 1:1; or melted unsalted butter 1:1 (a little richer, a bit denser).
Canned pumpkin puree: Adds moisture and pumpkin flavor.
Large eggs (batter): Bind and add structure. Substitution: If you are short an egg, use ¼ cup plain yogurt per missing egg; texture will be a little denser but still good.
Chocolate chips: Add pockets of chocolate and a bakery look on top. Substitution: Semi-sweet, dark or milk chocolate chips 1:1, or an equal amount of chopped chocolate.
Cream cheese (brick style): Creates the tangy, creamy topping. Do not use whipped/tub cream cheese.
Brown sugar (topping): Sweetens the cheesecake layer with a hint of molasses. Substitution: ⅓ cup granulated sugar + 1 teaspoon molasses in place of ⅓ cup of brown sugar.
Egg (topping): Sets the cheesecake layer so it bakes creamy, not runny.
Vanilla extract: Rounds out the flavor in the topping. Substitution: Use imitation vanilla or simply omit.
Instructions
- Mix the muffin batter. In a large bowl, whisk together the flour, baking powder, baking soda, salt, and pumpkin spice. In a separate bowl, whisk the sugar, oil, pumpkin, eggs, and water until smooth, then fold the wet ingredients into the dry until just combined. Stir in the chocolate chips.
- Make the cheesecake topping. In another bowl, beat the cream cheese, brown sugar, egg, and vanilla extract until smooth.
- Assemble the muffins. Divide the muffin batter into a prepared muffin pan, filling each cup about three-quarters full. Spoon a little cream cheese mixture on top of each muffin, swirl gently, and sprinkle with extra chocolate chips.
- Bake and cool. Bake until a toothpick inserted in the center comes out with a few moist crumbs. Let muffins cool briefly in the pan, then transfer to a wire rack.
Variations
Gluten-Free: Substitute 1:1 gluten-free all-purpose flour blend in place of regular flour.
Nut-Free: Already is.
Dairy-Free: Use dairy-free cream cheese in the topping and dairy-free chocolate chips.
Vegan: Not recommended. The recipe relies on eggs for both structure and the cheesecake topping; look for a highly rated vegan pumpkin muffin recipe instead.
Make Ahead: Whisk dry ingredients and store at room temperature. Mix wet ingredients and store covered in the refrigerator up to 24 hours. Combine and assemble just before baking. Cheesecake topping can also be prepared up to 2 days in advance.
Equipment
Muffin pan: Essential for baking muffins. Standard 12-cup works best.
Electric Mixer: Makes the cheesecake topping smooth and lump free. A stand mixer is easiest, but a hand mixer or sturdy whisk also works.
Cooling Rack: Helps the muffins cool quickly and evenly. If you do't have one, transfer to a clean towel-lined counter.
Storage
Refrigerate: Store muffins in an airtight container in the fridge for up to 4 days. The cream cheese topping makes refrigeration necessary.
Freeze: These muffins freeze well. Allow them to cool completely, then wrap each muffin tightly in plastic wrap and place in a freezer-safe bag or container for up to 2 months. Thaw overnight in the refrigerator before serving.
Reheat: For best texture, warm in a 300°F oven for 8–10 minutes until heated through. Muffins can also be microwaved in 20–30 second intervals, though the topping may soften more than when reheated in the oven.
FAQ's
Yes, as long as it is thick and wet-drained. Watery puree will make the muffins dense.
No, but they make cleanup easier and help the muffins release cleanly. If you skip liners, be Sure to coat the muffin pan thoroughly with nonstick spray.
Yes. Bake the muffins without the topping for a classic pumpkin chocolate chip muffin.
Yes, the recipe doubles well. Bake in two muffin pans on the same rack or rotate pans halfway through baking.
Related
Looking for other recipes like this? Try these:
Pairing
These are my favorite dishes to serve with cheesecake pumpkin muffins:
Recipe
Pumpkin Cheesecake Muffins
- Total Time: 35 minutes
- Yield: 15 muffins
Ingredients
For Pumpkin Muffins
All-purpose flour (1 ½ cups | 212g)
Baking powder (1 teaspoon | 4g)
Baking soda (½ teaspoon | 3g)
Salt (¾ teaspoon | 4.5g)
Pumpkin pie spice (2 ¼ teaspoon | 5.5g)
Granulated sugar (1 ¼ cups | 250g)
Vegetable oil (½ cup | 120ml)
Canned pumpkin puree (1 cup | 240g)
Large eggs (2 | ~100g)
Water (¼ cup | 60ml)
Regular chocolate chips (¾ cup | 135g + extra for topping)
For Cheesecake Topping
Cream cheese (8 oz | 226g, room temperature)
Brown sugar (⅓ cup | 67g)
Egg (1 | ~50g)
Vanilla extract (1 teaspoon | 5ml)
Instructions
- Preheat the oven to 350°F. Coat a muffin pan with nonstick spray or line with muffin liners.
- In a large mixing bowl, whisk together all-purpose flour (1 ½ cups), baking powder (1 tsp), baking soda (½ tsp), salt (¾ tsp), and pumpkin pie spice (2 ¼ tsp) until well combined.
- In a medium bowl, whisk granulated sugar (1 ¼ cups), vegetable oil (½ cup), canned pumpkin puree (1 cup), large eggs (2), and water (¼ cup) until smooth.
- Pour the pumpkin mixture into the dry ingredients and fold gently with a spatula until just combined. Do not overmix.
- Stir in chocolate chips (¾ cup) until evenly distributed.
- Divide the pumpkin batter evenly into the prepared muffin cups, filling each about ¾ full.
- In the bowl of a stand mixer or a medium bowl with an electric mixer, beat together cream cheese (8 oz), brown sugar (⅓ cup), egg (1), and vanilla extract (1 tsp) until smooth and fully combined.
- Add 1–2 tablespoons of the cream cheese mixture on top of each muffin using the same scoop. Swirl gently if desired.
- Sprinkle the tops with additional chocolate chips.
- Bake for 20–22 minutes, until a toothpick inserted into the muffin comes out with a few moist crumbs.
- Let the muffins cool in the pan for 5 minutes, then transfer to a wire rack to cool completely. Store in an airtight container at room temperature for up to 4 days.
- Prep Time: 15 minutes
- Cook Time: 20 minutes
- Category: Breakfast
- Method: Baking
- Cuisine: American
Ann
WOW! These muffins are fantastic! I like that they’re naturally sweetened, super moist, and wholesome. They would be perfect for breakfast or as dessert for afternoon tea. I’m sure they taste like heaven. I’ll probably give these a try next weekend. Gonna follow your recipe precisely.
Bailey, thank you so much for answering all of the possible questions and all of your useful recommendations. The info you provide will surely help me and your readers a lot. Look forward to your new awesome ideas. Your blog is wonderful!