These Pumpkin Cream Cheese Muffins are my homemade version of the seasonal Starbucks favorite—and honestly, I think they’re even better. They’re moist, warmly spiced, and filled with rich pumpkin flavor, all topped with a luscious pocket of sweet cream cheese and a sprinkle of crunchy pepitas. Perfect for cozy mornings, fall gatherings, or whenever I’m craving a bakery-style treat from home.

Why You’ll Love This Recipe

I love this recipe because it’s simple to make but tastes like it came straight from a coffee shop. The muffin base is soft and flavorful with cinnamon and pumpkin spice, and the cream cheese center adds the perfect creamy contrast. It’s just sweet enough without being over-the-top, and that little crunch from the seeds on top gives every bite a great finish. These muffins freeze well too, so I always make a double batch.

ingredients

(Here’s a tip: Check out the full list of ingredients and measurements in the recipe card below.)

For the muffins:

• All-purpose flour
• Baking soda
• Baking powder
• Salt
• Ground cinnamon
• Pumpkin pie spice
• Granulated sugar
• Brown sugar
• Pumpkin puree (not pumpkin pie filling)
• Eggs
• Vegetable oil (or melted coconut oil)
• Vanilla extract

For the cream cheese filling:

• Cream cheese, softened
• Granulated sugar
• Vanilla extract

For the topping:

• Raw pumpkin seeds (pepitas)
• Optional: coarse sugar for extra crunch

directions

1. I preheat the oven to 350°F (175°C) and line a muffin tin with paper liners.
2. In a large bowl, I whisk together the flour, baking soda, baking powder, salt, cinnamon, and pumpkin pie spice.
3. In another bowl, I whisk the granulated sugar, brown sugar, eggs, pumpkin puree, oil, and vanilla until smooth.
4. I pour the wet ingredients into the dry and gently fold everything together just until combined—being careful not to overmix.
5. In a small bowl, I beat the cream cheese, sugar, and vanilla until smooth and creamy.
6. I fill each muffin liner about ¾ full with the pumpkin batter.
7. Using a spoon or piping bag, I add a small dollop (about 1 tablespoon) of the cream cheese mixture into the center of each muffin. I don’t press it down too far—it will settle as the muffins bake.
8. I sprinkle the tops with pumpkin seeds (and coarse sugar if using).
9. I bake for 18–22 minutes, or until the muffins are set and a toothpick inserted around the edge comes out clean.
10. I let them cool in the pan for 5 minutes before transferring to a wire rack.

Servings and timing

This recipe makes 12 regular-sized muffins.
Prep time takes about 15 minutes, and bake time is 18–22 minutes.
From start to finish, I have fresh pumpkin cream cheese muffins ready in just about 40 minutes.

Variations

Sometimes I use a maple cream cheese filling by adding a teaspoon of maple syrup to the mix. I’ve also made mini muffins with a tiny swirl of filling for a bite-sized treat. If I’m feeling extra indulgent, I top them with a drizzle of cream cheese glaze once cooled. For a healthier twist, I substitute half the oil with applesauce and cut back slightly on the sugar.

storage/reheating

I store these muffins in an airtight container in the fridge for up to 5 days. I like to bring them to room temperature or warm them for about 10 seconds in the microwave before serving. They also freeze beautifully—I wrap them individually and freeze for up to 2 months. I thaw them overnight in the fridge or reheat gently straight from frozen.

FAQs

Can I use pumpkin pie filling instead of puree?

No, I stick with pure pumpkin puree because pumpkin pie filling is pre-sweetened and spiced, which would throw off the flavor and texture.

How do I get the cream cheese to stay in the center?

I keep the cream cheese mixture thick, and I drop it gently on top of the batter—then let it settle naturally while baking. It will sink slightly as it cooks.

Can I make these gluten-free?

Yes, I use a 1:1 gluten-free flour blend and make sure my baking powder and soda are gluten-free. The texture stays nice and moist.

Why are my muffins dense?

That usually means the batter was overmixed. I stir gently just until combined—lumps are okay. Also, make sure your baking soda is fresh.

Can I skip the pumpkin seeds?

Of course. The muffins are still delicious without them, but I love the added crunch and visual appeal they give.

Conclusion

These Pumpkin Cream Cheese Muffins are the ultimate fall bakery-style treat—soft, spiced, and filled with creamy goodness in every bite. I love how easy they are to make from scratch, and they taste just like (or better than) the ones from Starbucks. Whether for breakfast, dessert, or a cozy snack, they always bring warmth and comfort to the season.