Fluffy and moist pumpkin muffins filled with a cream cheese center and topped with a cinnamon sugar pecan crunch, these Pumpkin Cream Cheese Muffins are perfect for fall.

Pumpkin Puree vs. Pumpkin Pie filling
Make sure when you buy your pumpkin puree, that it is 100% pumpkin not pumpkin pie filling which has other ingredients added in.
What muffin pan should I use?
I love making jumbo muffins using this large muffin pan but you can also make them in this standard muffin pan.
Can I leave out the Pecans?
Yes! You can leave out the pecans, or swap them for walnuts or pumpkin seeds.
Tips for making a Pumpkin Muffins
- Be sure to actually brown the butter. First it’ll be loud, then quiet and foamy – this is when you’ll want to stir it. Then brown bits should start to appear. Let it cook for another 30 seconds once you start to see brown.
- It can be kind of hard to tell when the muffins are finished baking because of the cream cheese center. Make sure you are using an oven thermometer to bake these at the correct temperature.
- If you don’t have properly sized muffin liners, just cut large squares of parchment paper and press it into the muffin pan to give it a bit of muscle memory.
- The key to getting tall muffin tops is to only bake a muffin in every other muffin cup, fill the muffin cups to the top with the batter, and first bake them at a high temperature.
- Make sure to preheat the oven before starting to mix the muffin batter. It will come together quite quickly. That being said you can prep this batter hours ahead of time just cover it and place it in the fridge until you’re ready to use it.
- If you don’t want to add pecans you can swap them for walnuts, pumpkin seeds, or just leave them out!
- I love making jumbo muffins using this large muffin pan but you can also make them in this standard muffin pan. If using a standard muffin pan, you’ll want to bake these for a total of 12 minutes instead of 16 minutes.
Additional Recipes to try!

Pumpkin Muffin Ingredients
- Butter: I like to use salted butter for this recipe but unsalted butter will work too!
- Sugar: These muffins use regular white sugar and dark brown sugar in the batter and white sugar in the filling and on top.
- Pumpkin Pie Spice: I do get a little lazy and use store bought pumpkin pie spice but you can also make your own!
- Cinnamon: A bit of ground cinnamon is added into the topping mixture for a bit of extra spice.
- Pumpkin Puree: As mentioned above, be sure to use pumpkin puree which is 100% pumpkin and not pumpkin pie filling.
- Eggs: I use standard large eggs from the store.
- Salt: A little bit of fine sea salt enhances the flavors and balances out the sweetness.
- Vanilla Extract: Vanilla enhances the flavor of the muffins and the filling.
- Flour: Any all purpose flour will work for this recipe!
- Baking soda & powder: Both baking soda and baking powder play a role in how the muffins rise so make sure neither is expired!
- Pecans: I love adding toasted pecans into the pumpkin batter and on top but of course walnuts or pumpkin seeds would work too! Or you can leave them out all together.
- Cream Cheese: Be sure to use standard full fat cream cheese for the best texture! It’s easiest to mix and use when it is at room temperature.
How to make Cream Cheese Pumpkin Muffins?
Brown Butter
- Add the pumpkin pie spice into a medium heat safe mixing bowl.
- In a medium stainless pot, add in the salted butter. Cook over medium low heat.
- The butter will first melt, then it will get noisy and bubble. After a couple minutes, the noise will go away and it will begin to foam.
- At this point you can start to stir it occasionally. The butter will start to brown, cook for an additional 30 seconds to a minute until brown bits start to foam to the top.
- Turn off the heat and pour the brown butter over the pumpkin pie spice into the mixing bowl. Stir to combine and set aside for 5 minutes to cool off slightly.
- Preheat the oven to 425 F and place a rack in the center.
Pecans & the topping
- Pour the pecans into a large shallow pan, place over low heat, tossing regularly.
- Toast until the pecans feel quite warm to the touch, make sure you don’t burn them – their color shouldn’t change at all.
- Immediately remove them from the heat and give them a rough chop.
- Set aside 100 g of the chopped pecans, mix the remaining pecans with the sugar and cinnamon for the topping in a small bowl
Pumpkin Muffin Batter
- Line every other cup in the muffin pan. If you’re using the jumbo muffin pan and don’t have the right sized liners, just cut large squares of parchment paper and press it into the muffin pan to give it a bit of muscle memory.
- Add both sugars, salt, and vanilla into the bowl with the brown butter and whisk to combine. Then add in the pumpkin puree, whisk again, and then both eggs and whisk once more.
- Pour in the all purpose flour along with the baking soda and baking powder right on top of the flour.
- Use the whisk to first whisk the baking soda and baking powder into the flour and then completely in with the wet ingredients.
- Pour in the remaining pecans and use a rubber spatula to fold them in.
Cream Cheese filling
- In a medium mixing bowl add in the room temperature cream cheese, sugar, salt, and vanilla. Use an electric mixer or a spoon to mix until smooth – be careful not to whip it full of air.
Assemble & Bake the Pumpkin Muffins
- Fill every other muffin cup (aka only the ones you’ve lined) about 90% full with the pumpkin batter.
- Add the cream cheese filling into a piping bag or a plastic zip top bag. Press the tip of the bag into the center of the muffins, almost all the way to the bottom.
- Start squeezing the filling out, while lifting the bag slowly until you reach the top.
- Sprinkle the top of each muffin, around the cream cheese center, with the cinnamon sugar pecan mixture.
- I only have one jumbo pan so I bake half the batter, leave the rest of the batter in the bowl at room temperature, then bake the remaining batter once the first half has baked.
- Place the muffin pan in the hot oven and bake for 8 minutes. After the 8 minutes, turn the oven down to 350 and bake for another 6-8 minutes.
- Once baked, take the pan out of the oven. Turn the oven back up to 425 F and leave the freshly baked muffins to cool for 5 minutes before carefully lifting them out of the pan.
- Let the pan cool off while the oven turns up, then repeat the assembly process with the remaining pumpkin batter. Bake according to the above instructions.
- Allow the muffins to cool for at least 10 minutes once removed from the pan so that you don’t burn your mouth on the cream cheese.
- Store leftovers in an airtight container either at a cool room temperature or in the fridge!

Pumpkin Cream Cheese Muffins
Equipment
Ingredients
Pumpkin Batter
- 180 grams salted butter
- 5 teaspoons pumpkin pie spice
- 80 grams dark brown sugar
- 80 grams granulated sugar
- 1/4 teaspoon fine sea salt
- 1 teaspoon vanilla extract
- 275 grams pumpkin puree
- 2 eggs standard large, room temperature
- 300 grams all purpose flour
- 1 teaspoon baking soda
- 1 teaspoon baking powder
Pecans & topping
- 130 grams pecans
- 35 grams granulated sugar
- 1 teaspoon cinnamon
Cream Cheese Filling
- 226 grams cream cheese room temperature
- 40 grams granulated sugar
- 1/4 teaspoon fine sea salt
- 1 teaspoon vanilla extract
Instructions
Brown Butter
- Add the pumpkin pie spice into a medium heat safe mixing bowl.
- In a medium stainless pot, add in the salted butter. Cook over medium low heat.
- The butter will first melt, then it will get noisy and bubble. After a couple minutes, the noise will go away and it will begin to foam.
- At this point you can start to stir it occasionally. The butter will start to brown, cook for an additional 30 seconds to a minute until brown bits start to foam to the top.
- Turn off the heat and pour the brown butter over the pumpkin pie spice into the mixing bowl. Stir to combine and set aside for 5 minutes to cool off slightly.
- Preheat the oven to 425 F and place a rack in the center.
Pecans & the Topping
- Pour the pecans into a large shallow pan, place over low heat, tossing regularly.
- Toast until the pecans feel quite warm to the touch, make sure you don’t burn them – their color shouldn’t change at all.
- Immediately remove them from the heat and give them a rough chop.
- Set aside 100 g of the chopped pecans, mix the remaining pecans with the sugar and cinnamon for the topping in a small bowl.
Pumpkin Muffin Batter
- Line every other cup in the muffin pan. If you're using the jumbo muffin pan and don't have the right sized liners, just cut large squares of parchment paper and press it into the muffin pan to give it a bit of muscle memory.
- Add both sugars, salt, and vanilla into the bowl with the brown butter and whisk to combine. Then add in the pumpkin puree, whisk again, and then both eggs and whisk once more.
- Pour in the all purpose flour along with the baking soda and baking powder right on top of the flour.
- Use the whisk to first whisk the baking soda and baking powder into the flour and then completely in with the wet ingredients.
- Pour in the remaining pecans and use a rubber spatula to fold them in.
Cream Cheese Filling
- In a medium mixing bowl add in the room temperature cream cheese, sugar, salt, and vanilla. Use an electric mixer or a spoon to mix until smooth – be careful not to whip it full of air.
Assemble & Bake
- Fill every other muffin cup (aka only the ones you've lined) about 90% full with the pumpkin batter.
- Add the cream cheese filling into a piping bag or a plastic zip top bag. Press the tip of the bag into the center of the muffins, almost all the way to the bottom.
- Start squeezing the filling out, while lifting the bag slowly until you reach the top.
- Sprinkle the top of each muffin, around the cream cheese center, with the cinnamon sugar pecan mixture.
- I only have one jumbo pan so I bake half the batter, leave the rest of the batter in the bowl at room temperature, then bake the remaining batter once the first half has baked.
- Place the muffin pan in the hot oven and bake for 8 minutes. After the 8 minutes, turn the oven down to 350 and bake for another 6-8 minutes.
- Once baked, take the pan out of the oven. Turn the oven back up to 425 F and leave the freshly baked muffins to cool for 5 minutes before carefully lifting them out of the pan.
- Let the pan cool off while the oven turns up, then repeat the assembly process with the remaining pumpkin batter. Bake according to the above instructions.
- Allow the muffins to cool for at least 10 minutes once removed from the pan so that you don't burn your mouth on the cream cheese.
- Store leftovers in an airtight container either at a cool room temperature or in the fridge!
Notes
- Be sure to actually brown the butter. First it’ll be loud, then quiet and foamy – this is when you’ll want to stir it. Then brown bits should start to appear. Let it cook for another 30 seconds once you start to see brown.
- It can be kind of hard to tell when the muffins are finished baking because of the cream cheese center. Make sure you are using an oven thermometer to bake these at the correct temperature.
- If you don’t have properly sized muffin liners, just cut large squares of parchment paper and press it into the muffin pan to give it a bit of muscle memory.
- The key to getting tall muffin tops is to only bake a muffin in every other muffin cup, fill the muffin cups to the top with the batter, and first bake them at a high temperature.
- Make sure to preheat the oven before starting to mix the muffin batter. It will come together quite quickly. That being said you can prep this batter hours ahead of time just cover it and place it in the fridge until you’re ready to use it.
- If you don’t want to add pecans you can swap them for walnuts, pumpkin seeds, or just leave them out!
- I love making jumbo muffins using this large muffin pan but you can also make them in this standard muffin pan. If using a standard muffin pan, you’ll want to bake these for a total of 12 minutes instead of 16 minutes.
Nutrition
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Hi! I was wondering about how much butter you end up with after it has been browned. Because I use cheap Aldi butter and I noticed that it reduces down really significantly. I made your brown butter chocolate chip pumpkin bread recipe and it turned out a little dry. I was wondering if my cheap butter had a higher water content than the high quality Irish butter and reduced down more than yours or something. Then again, maybe I got fooled by the chocolate chips in that recipe and over baked it!
Hi! I was wondering about how much butter you end up with after it has been browned. Because I use cheap Aldi butter and I noticed that it reduces down really significantly. I made your brown butter pumpkin bread recipe and it turned out a little dry. I was wondering if my cheap butter had a higher water content than the high quality Irish butter and reduced down more than yours or something. Then again, maybe I got fooled by the chocolate chips in that recipe and over baked it!
That looks amazing I can’t wait to try it!
I have a question about the amount of spices used in the recipe. I read that it has 5 teaspoons of pumpkin pie spice, and wondered if that would be too powerful or not?
And thank you!
Excellent, I used Pepitas and walnuts. A winner.
4.5 stars
Followed the recipe to a T; I would’ve preferred more cream cheese filling, because it was SO good! The texture of the muffin itself was a tiny bit granular and I think I wouldn’t have noticed that it I had more cream cheese.
Thank you for an easy to follow recipe!