Pumpkin Cream Cheese Muffins

These Pumpkin Cream Cheese Muffins are soft, moist, and perfectly spiced! They come together in one bowl in under 35 minutes. An easy vanilla cream cheese filling is baked right into the middle and tastes even better than Starbucks!

This is a super-soft, moist pumpkin cream cheese muffin like Starbucks’ but without the artificial flavorings and preservatives. Cream cheese has an absolutely exquisite tanginess to it, which adds a lovely balance, just like it does in my cream cheese chocolate chip cookies!

This is an easy muffin recipe that comes together in one bowl with a whisk! You could certainly swirl the cream cheese into the batter as I did with this Nutella banana bread or bake it in a loaf like this moist pumpkin bread. You could also try my healthy pumpkin muffins to mix it up.

Ingredients & Substitutions

• Light Brown Sugar: Sweetens the batter and adds a subtle molasses depth that complements the pumpkin. It also contributes to a slightly moist, tender crumb you can use dark brown sugar if that’s what you have.
• Vegetable Oil: Keeps the muffins moist at room temperature longer than butter would. Do not substitute melted butter 1:1 without expecting a denser, firmer crumb; you could use another oil, just know coconut oil or olive oil will impart a flavor. If pumpkin and olive oil sounds delicious, try my pumpkin olive oil cake!
• Pumpkin Puree: This is the ingredient I am most particular about: I use Libby’s canned pumpkin puree, not pumpkin pie filling. The recipe calls for half of a 15-ounce can, so you will have the other half for healthy pumpkin muffins. If you use homemade puree, drain it thoroughly, or the batter will be too loose.
• Baking Soda and Baking Powder: Work together here because the batter has both acidic ingredients (brown sugar, pumpkin) and neutral ones. Using both gives the muffins a full, even rise without a metallic aftertaste.
• Sugar: There is a significant amount of granulated sugar in this recipe. It is part of what makes the crumb so tender and light and makes these muffins taste like Starbucks. You can substitute coconut sugar for both the granulated and light brown sugar for a healthier alternative.
• Pumpkin Spice Mix: A full tablespoon and a half of spice mix gives this batter its warmth and depth. I use my Pumpkin Spice Recipe, but the recipe notes include exact individual spice measurements if you want to measure for this batch only, or you can use store-bought.
• Cream Cheese: I use Philadelphia’s brick-style cream cheese in this sweet cream cheese filling. For the best texture use full fat cream cheese and not low fat or whipped.

Variations on Pumpkin Cream Cheese Muffins

• Add a crumble. Add the crumble topping from this pumpkin coffee cake for a sweet, spiced topping, or make this easy brown sugar streusel topping recipe with a dash of pumpkin pie spice! You could even add in some pumpkin seeds, pecans or walnuts for an added crunch.
• Bake into loaf pans. This same recipe will yield two loaves of pumpkin bread. Perhaps consider making 1.5x the cream cheese filling recipe for a more substantial swirl.
• Swirl the cream cheese filling. Swirl the cheesecake filling for an easy pumpkin cream cheese swirl muffin. It’s such an excellent flavor combo that I even top my pumpkin cupcakes with a maple cream cheese buttercream!

Professional Tips for Making Pumpkin Cream Cheese Muffins

• Do not overmix the batter. The biggest mistake people make is over-mixing their muffin batter. Just because you can mix it all with a whisk, doesn’t mean you should. Over-mixing leads to too much gluten development, which can correspondingly make muffins tough. I always fold in the dry ingredients with a rubber spatula.
• Use a cookie scoop to portion. In this recipe I use a large cookie scoop to fill the muffin tins with batter and a small scoop to dollop on the cream cheese filling. This ensures a nice even shape and distribution!
• Press the cream cheese filling in slightly. After scooping the filling onto the center of each muffin, press it down just enough so the batter begins to come up around the sides. This is what keeps it centered during baking rather than sitting on top and browning.
• Use full-fat block cream cheese at the right temperature. It should be softened enough to beat smooth but not so warm that it loses its structure. I tested this at a range of temperatures and found that cream cheese pulled from the refrigerator 20 to 30 minutes before mixing hits the right balance: smooth enough to pipe cleanly, firm enough to hold its shape in the oven.

How to Make Pumpkin Cream Cheese Muffins

Start with the cream cheese filling so it has a few minutes to firm back up in the refrigerator while you mix the muffin batter. Further details and measurements can be found in the recipe card below.

Step 1: Preheat the oven and prepare the pan. Set your oven to 350°F and line a standard 12-cup muffin tin with paper liners.

Make Cream Cheese Filling

Step 2: Make the cream cheese filling. Beat the cream cheese with the granulated sugar until smooth, then mix in the vanilla. If your cream cheese is slightly softened, this comes together easily by hand with a spatula, which is what I usually do. You are looking for a completely lump-free mixture that holds its shape when scooped. (photos 1 & 2).

If your cream cheese is still cold from the refrigerator, it will be harder to beat smooth and may leave small lumps in the filling. Let it sit at room temperature for 10 to 15 minutes before you start.

Make Muffin Batter

Step 3: Whisk the dry ingredients. Add the flour, baking soda, baking powder, salt, and pumpkin spice to a medium bowl and whisk them together until evenly combined. (photo 3 & 4).

Step 4: Mix the wet ingredients. In a large bowl, whisk together the light brown sugar, granulated sugar, oil, and eggs until smooth, then whisk in the pumpkin puree. The mixture will look glossy and pourable, with the pumpkin turning everything a deep orange, which is exactly what you want to see. (photos 5-8).

For the best emulsion whisk the eggs then slowly add the oil until completely combined. Then add the sugars and pumpkin puree.

Step 5: Fold in the dry ingredients. Add the dry ingredients to the wet and fold with a spatula until just combined. Stop as soon as you no longer see dry streaks of flour. Overmixing activates gluten and will make your muffins dense and tough rather than tender, so a few small streaks disappearing on the last fold is perfectly fine. (photos 9 & 10).

Divide and Bake

Step 6: Fill the muffin cups and add the cream cheese. Divide the batter evenly between the 12 lined cups, filling each about two-thirds full. Using a small cookie scoop (roughly an inch wide), place one round of cream cheese filling directly in the center of each muffin and press it down slightly so it nestles into the batter. The cream cheese will not disappear completely during baking, and that is fine — you want that visible swirl on top. (photo 11).

If you refrigerate the cream cheese filling while mixing the batter, it will hold its shape much better when you scoop it, giving you cleaner circles on every muffin.

Step 7: Bake until just set. Bake at 325°F convection or 350°F conventional for about 20 minutes. Start checking at 18 minutes. The muffins are done when a toothpick inserted into the pumpkin portion comes out with a few moist crumbs clinging to it, or when the tops spring back lightly when you press them. The cream cheese center will look slightly puffed and matte rather than glossy, which is exactly what you want to see. (photo 12).

Avoid testing through the cream cheese center when checking doneness — you will always get a wet result there. Angle the toothpick into the pumpkin batter on the side of the muffin for an accurate read.

Step 8: Cool and serve. Let the muffins rest in the pan for 5 minutes before transferring them to a wire rack. The cream cheese filling will be very soft straight from the oven and needs a few minutes to firm back up. They are best served once the filling has set, about 20 minutes out of the oven, though they are equally good at room temperature the next day. (photo 13).

Recipe FAQs

Before You Go

I hope you enjoyed this professional chef tested recipe. Check out our other delicious, chef-developed muffin recipes like these morning glory muffins, or dive into more pumpkin with 10 Easy Pumpkin Recipes you must make this Fall!