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These Cheesecake Pumpkin Muffins are a delicious fall treat! Tender spiced pumpkin muffins with a silky vanilla cheesecake middle. Yields 18 muffins in under an hour.

Our Youngest Turns 21 on Monday.
It’s crazy to think she was 6 years old when I started this blog. Malloree is my go-to dessert recipe taste-tester (since our oldest is at college) so I find it truly fitting to share something she loves: a pumpkin dessert. When I asked her how she would describe these cheesecake pumpkin muffins she said “they are the best thing ever!” – not really what I was looking for but she does speak the truth.
Essentially a silky cheesecake filling is sandwiched between a moist pumpkin spiced muffin. Not too overly sweet to have for breakfast, but just extra enough for dessert. In a nutshell? It’s exactly what Malloree described them as.


Super simple and if you haven’t started your fall baking, I highly recommend starting with this one!


To Make These Pumpkin Cheesecake Muffins You Will Need:
- unbleached all-purpose flour – Gives structure to the muffins.
- pumpkin spice – Use homemade or store-bought.
- ground ginger – Lends warmth and is spicy with slightly sweet flavor and a subtle peppery kick.
- baking soda – Creates a gas which helps the batter to rise while baking.
- fine sea salt – Use either sea salt or pink himalayan.
- eggs – Set out 30 minutes before using or let sit in a bowl of lukewarm water.
- granulated sugar – For sweetening and flavor.
- pumpkin puree – Use 100% pure pumpkin puree and not pumpkin pie filling.
- olive oil – Adds moisture to the batter. I like to use a neutral oil like extra-light olive oil.
- unsweetened applesauce – A little trick for adding moisture without the extra fat.
- pure vanilla extract – Adds warmth and enhances all of the other flavors in this recipe.


Preheat your oven to 375℉ (or 190℃).
Line a standard muffin pan plus half of a second pan with 18 paper cupcake or muffin liners.


Make The Muffin Batter:
Next, in a large mixing bowl, measure and add 3 cups unbleached all-purpose flour, 1 tablespoon pumpkin spice, 1/2 teaspoon ground ginger, 2 teaspoons baking soda and 1 teaspoon fine sea salt.


Whisk to combine.


In a separate bowl, measure and add 4 large eggs, 1-1/2 cups granulated sugar, 1 and 3/4 cup pumpkin puree or 1 (15 ounce) can, 1 cup extra light olive oil, 1/2 cup unsweetened apple sauce and 1-1/2 teaspoons pure vanilla extract.


Again, whisk well to combine.


Pour the pumpkin mixture into the bowl with the dry.


Switch to a spatula and mix until the flour is incorporated.


Set this off to the side for a moment.


Make the cream cheese filling:
Combine 8 ounces softened cream cheese with 1 egg and 1 teaspoon pure vanilla extract. If you desire more of a sweetened cheesecake filling, mix in 1 tablespoon granulated sugar.


Measure and drop 2 tablespoons of the pumpkin batter into each of the paper liners.


Tap on the countertop to settle it a bit.


Divide the cheesecake filling (about 1 tablespoon per muffin) top the pumpkin batter.


Lastly, top with 2 more tablespoons of the pumpkin batter.
Slip the pans into your oven and bake for 18 to 22 minutes. Rotate the pans halfway through baking.


The tops of each muffin should be lightly golden and when a cake tester is inserted, only a few crumbs come back attached.


Let cool before serving with coffee or your favorite tea.


Click Here For More Pumpkin Recipes!


Enjoy! And if you give this Cheesecake Pumpkin Muffins recipe a try, let me know! Snap a photo and tag me on twitter or instagram!


Yield: 18 muffins
Cheesecake Pumpkin Muffins
These Cheesecake Pumpkin Muffins are a delicious fall treat! Tender spiced pumpkin muffins with a silky vanilla cheesecake middle. Yields 18 muffins in under an hour.
FOR THE MUFFINS:
- 3 cups unbleached all-purpose flour
- 1 tablespoon pumpkin spice
- 1/2 teaspoon ground ginger
- 2 teaspoons baking soda
- 1 teaspoon fine sea salt
- 4 large eggs
- 1½ cups granulated sugar
- 1¾ cups 100% pure pumpkin purée
- 1 cup olive oil, extra light tasting
- 1/2 cup unsweetened applesauce
- 1½ teaspoon vanilla extract
FOR THE CHEESECAKE FILLING:
- 8 ounces cream cheese, softened
- 1 large egg
- 1 teaspoon vanilla extract
- 1 tablespoon sugar, optional
PREPARE THE PUMPKIN BATTER:
-
Preheat your oven to 375℉ (or 190℃).
-
Line a standard muffin pan and half of another with paper liners.
-
Next, in a large mixing bowl, measure and add flour, pumpkin spice, ground ginger, baking soda and fine sea salt. Whisk to combine.
-
In a separate bowl, measure and add eggs, sugar, pumpkin puree, olive oil, unsweetened apple sauce and pure vanilla extract. Whisk to combine.
-
Pour the pumpkin mixture into the bowl with the dry. Switch to a spatula and mix until the flour is incorporated. Set this off to the side for a moment.
PREPARE THE CHEESECAKE FILLING:
-
In a mixing bowl, combine softened cream cheese, egg and vanilla extract. If you desire more of a sweetened cheesecake filling, mix in 1 tablespoon granulated sugar.
-
In your prepared pan, measure and drop 2 tablespoons of the pumpkin batter into each of the paper liners. Tap on the countertop to settle it a bit.
-
Divide the cheesecake filling (about 1 tablespoon per muffin) top the pumpkin batter.
-
Lastly, top with 2 more tablespoons of the pumpkin batter.
-
Slip the pans into your oven and bake for 18 to 22 minutes. Rotate the pans halfway through baking. The muffins are done when a tester is inserted and only a few crumbs come out attached.
-
Let cool before serving.
Nutrition Disclaimer: All information presented on this site is intended for informational purposes only. I am not a certified nutritionist and any nutritional information shared on SimplyScratch.com should only be used as a general guideline.
Serving: 1muffin, Calories: 326kcal, Carbohydrates: 37g, Protein: 5g, Fat: 18g, Saturated Fat: 5g, Polyunsaturated Fat: 2g, Monounsaturated Fat: 10g, Trans Fat: 1g, Cholesterol: 66mg, Sodium: 313mg, Potassium: 117mg, Fiber: 1g, Sugar: 19g, Vitamin A: 3955IU, Vitamin C: 1mg, Calcium: 32mg, Iron: 2mg
This recipe was originally posted on October 6th, 2021 and has been updated with clear and concise instructions, new photography and helpful information.
This post may contain affiliate links.
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Laurie McNamara
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