Pumpkin cheesecake muffins are a pumpkin swirled cream cheese muffin with a spiced streusel crumb and pumpkin seed topping. They’re super moist and fluffy and taste like everything we love about the season!

pumpkin cream cheese muffins with crumb topping

Extra moist and fluffy with a spiced streusel topping, these pumpkin cheesecake muffins are truly the best muffin for fall! They pop out of the pan with a perfectly fluffy muffin top just like you would expect from a pumpkin muffin from a bakery, and will make your whole house smell amazing while they bake.

Typically on Once Upon a Pumpkin I make healthier versions of pumpkin recipes. I strive to bake up fun pumpkin treats with a little less sugar, perhaps made gluten free and or with just a few simple ingredients.

The thing about the fall is that it brings about a feeling of nostalgia that we look forward to all year. That comfort and coziness that comes from the smell of cinnamon, crisp air and golden hues. As a dietitian, I think I do a pretty good job of bringing that into my healthier pumpkin recipes, but sometimes you just can’t beat the real thing made with traditional ingredients.

That is the balance I preach through this site and on my Instagram page — nutrition that is about mindful choices that honor how you feel, are enjoyable and allow you to enjoy your life (and live your best fall life!).

These bakery-style pumpkin muffins will hopefully remind you of your love of all things fall, baking with your mom or grandma and taking in all the scents and flavors of the season.

This pumpkin recipe uses an entire can of pumpkin puree, and lots of fall spices that will have your whole house smelling amazing. The silky smooth cream cheese layer in between layers of fluffy pumpkin muffin is my favorite part!

So get out your cans of pumpkin, light a fall candle and let’s make these irresistible pumpkin cream cheese muffins!

Ingredients for Pumpkin Cheesecake Muffins with Streusel Topping

Organic All-purpose Flour or White Whole-Wheat Flour
Pumpkin Puree — this muffin recipes uses an entire can of pumpkin puree! Make sure it’s 100% pure pumpkin and not pumpkin pie mix.
Coconut Oil
Eggs + egg yolk
Light Brown Sugar
Pumpkin Spice
Cinnamon
Baking Soda
Baking Powder
Cream Cheese
Butter
Pumpkin Seeds

Equipment / utensils

mixing bowls
whisk
wooden spoon
muffin pan
muffin liners

Tips for Making the Best Pumpkin Muffins

Measure the flour correctly. Too much flour can definitely impact how these muffins turn out. Use a scoop to scoop flour into a measuring cup (don’t pack it in!) to ensure you don’t have too much.
Don’t over mix the batter. Muffin batter shouldn’t be super smooth. You want there to be bumps. Just as soon as you don’t see any major streaks of flour, stop mixing.
Make sure the baking soda and baking powder are fresh. This is a sneaky little thing I think a lot of us don’t think about. If your baking soda or baking powder has been sitting untouched since last fall when you baked something, this could be impacting your baked goods negatively. Check the date on the label!

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Pumpkin Cheesecake Muffins

Pumpkin cheesecake muffins are super fluffy, spiced just right and taste like everything we love about fall. Enjoy one with a cup of coffee for all the fall feels!

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Prep Time 15

Cook Time 25

Servings 12 muffins

Equipment

2 mixing bowls
1 Whisk
1 wooden spoon
1 muffin pan
12 muffin liners

Ingredients

For the pumpkin muffin batter

2 cups organic all-purpose flour
2 tsp. baking powder
1 tsp. baking soda
1/4 tsp salt
2 tsp. cinnamon
2 tsp. pumpkin pie spice
1 15 oz. can pumpkin puree
2 eggs at room temperature
1/2 cup coconut oil melted
1 cup light brown sugar
1 tsp vanilla extract

For the Streusel Topping

1/3 cup brown sugar
3 tbsp butter melted
2 tsp. pumpkin spice
1/4 tsp. salt
1/2 cup all-purpose flour

For the Cream Cheese Layer

8 oz cream cheese softened
1 egg yolk
1 tsp. vanilla extract

Instructions

Preheat the oven to 400 degrees F and line a muffin pan with muffin liners, lightly spraying the inside with baking spray or oil so that that the muffins don't stick to the liners.
Get out the cream cheese and butter to soften and bring to room temperature.
In a medium sized mixing bowl whisk together the flour, baking powder, baking soda, cinnamon, pumpkin spice and salt. Set aside.
In another medium sized bowl, whisk together the pumpkin puree, eggs, coconut oil, brown sugar and vanilla until smooth.
Add the dry ingredients to the wet and combine using a wooden spoon careful not to over mix.
Make the cream cheese mixture by beating together softened cream cheese, egg yolk and vanilla extract.
Use an ice cream scoop to scoop the muffin batter into the muffin liner so that they're about 1/3 of the way filled. Spoon about 1 tablespoon of the cream cheese on top and then cover with remaining pumpkin batter (it's ok if the batter doesn't completely cover the cream cheese batter).
Make the streusel topping by combining the brown sugar, pumpkin pie spice, salt and and flour. Add melted butter and use a fork to mix it around into crumbs — it shouldn't be a super fine consistency.
Sprinkle the crumb topping and pumpkin seeds if desired over each. Bake for 23-25 minutes (checking at 23 minutes). Let cool and enjoy!