Pumpkin cheesecake muffins are one of the favorite treats to bake, especially when the fall season rolls around. The combination of creamy cheesecake and spiced pumpkin just hits the spot, and I love that there are so many ways to make them.
Whether you’re looking for a gluten-free option, something keto-friendly, or even a quick and simple three-ingredient version, I’ve got a recipe that will suit your needs. These muffins are a perfect blend of indulgence and comfort, and I can’t wait to share all the different variations with you.
In this post, I’ll be diving into seven types of pumpkin cheesecake muffins, each with its own twist. From a rich, sourdough-based recipe to a light and fluffy vegan option, there’s something here for everyone.
If you’re watching your carbs or need a dairy-free version, I’ve got you covered with low-carb and vegan recipes too. And for those days when you need something quick and easy, the three-ingredient muffins are a game-changer. So, whether you’re baking for yourself or a crowd, these muffins will be a hit in any kitchen.
1. Keto Pumpkin Cheesecake Muffin Recipe
Ingredients
For the Muffins:
- 2 cups almond flour
- ½ cup granulated sweetener (like Swerve or erythritol)
- ½ teaspoon cinnamon
- ¼ teaspoon nutmeg
- ½ teaspoon baking soda
- ½ teaspoon salt
- 1 cup pumpkin puree
- ¼ cup melted butter (or coconut oil)
- 2 large eggs
- 1 teaspoon vanilla extract
For the Cheesecake Filling:
- 8 ounces cream cheese, softened
- ¼ cup powdered sweetener (like Swerve or erythritol)
- 1 teaspoon vanilla extract
Instructions
Preheat the Oven: Preheat your oven to 350°F (175°C) and line a muffin tin with paper liners or grease it well.
Prepare the Cheesecake Filling: In a medium bowl, beat the softened cream cheese, powdered sweetener, and vanilla extract until smooth. Set aside.
Mix Dry Ingredients: In a large mixing bowl, combine the almond flour, granulated sweetener, cinnamon, nutmeg, baking soda, and salt. Mix well.
Combine Wet Ingredients: In another bowl, whisk together the pumpkin puree, melted butter, eggs, and vanilla extract until fully combined.
Combine Mixtures: Pour the wet ingredients into the dry ingredients and stir until just combined. Do not overmix.
Fill Muffin Tin: Spoon about two-thirds of the muffin batter into each muffin cup. Then add a tablespoon of the cream cheese filling on top of each muffin batter portion. Use a toothpick or knife to swirl the cream cheese filling into the batter slightly.
Bake: Bake in the preheated oven for about 25 minutes or until a toothpick inserted into the center comes out clean.
Cool and Serve: Allow the muffins to cool in the pan for about 10 minutes before transferring them to a wire rack to cool completely.
2. Sough Dough Pumpkin Cheesecake Muffin Recipe
Ingredients
For the Cheesecake Filling:
- 8 oz cream cheese, softened
- 1/4 cup powdered sugar substitute
- 1 tsp vanilla extract
For the Pumpkin Muffins:
- 1 1/2 cups all-purpose flour
- 1/2 cup sourdough starter discard
- 1/2 cup granulated sugar
- 1/4 cup unsalted butter, melted
- 1 egg
- 1 cup pumpkin puree
- 1 tsp baking powder
- 1/2 tsp baking soda
- 1/2 tsp salt
- 1 tsp ground cinnamon
- 1/2 tsp ground ginger
- 1/4 tsp ground nutmeg
Instructions
Make the cheesecake filling: In a medium bowl, beat the cream cheese with the powdered sugar substitute and vanilla until smooth. Transfer to a piece of plastic wrap and shape into a log about 1 inch thick. Freeze for 1-2 hours until firm.
Make the pumpkin muffin batter: In a large bowl, whisk together the flour, sourdough starter, sugar, melted butter, egg, pumpkin puree, baking powder, baking soda, salt, cinnamon, ginger and nutmeg until just combined.
Assemble the muffins: Line a 12-cup muffin tin with paper liners. Scoop about 2 tbsp of the pumpkin batter into the bottom of each liner. Slice the frozen cheesecake log into 12 equal pieces. Place one piece of cheesecake into the center of each muffin cup. Top with the remaining pumpkin batter, filling the cups all the way to the top.
Bake: Preheat oven to 350°F. Bake for 20-25 minutes until a toothpick inserted in the center comes out clean. Allow to cool completely in the pan before removing.
Serve: These muffins are delicious at room temperature or chilled. Store leftovers in the refrigerator for up to 5 days.
3. Gluten Free Pumpkin Cheesecake Muffin Recipe
Ingredients
For the Muffins:
- 1 ½ cups gluten-free all-purpose flour (ensure it contains xanthan gum)
- ½ cup coconut sugar (or brown sugar)
- 1 teaspoon baking powder
- ½ teaspoon baking soda
- ½ teaspoon salt
- 1 teaspoon pumpkin pie spice (or a mix of cinnamon, nutmeg, and ginger)
- 1 cup pumpkin puree
- 2 large eggs
- ¼ cup melted coconut oil (or butter)
- 1 teaspoon vanilla extract
- ¼ cup milk (dairy or non-dairy)
For the Cheesecake Filling:
- 8 oz cream cheese, softened
- ¼ cup powdered sugar (or sugar substitute)
- 1 teaspoon vanilla extract
- 1 egg yolk
Instructions
Preheat the Oven: Preheat your oven to 350°F (175°C) and line a muffin tin with paper liners or grease it well.
Prepare the Cheesecake Filling: In a medium bowl, beat the softened cream cheese, powdered sugar, vanilla extract, and egg yolk until smooth. Set aside.
Mix Dry Ingredients: In a large mixing bowl, combine the gluten-free flour, coconut sugar, baking powder, baking soda, salt, and pumpkin pie spice. Whisk until well combined.
Combine Wet Ingredients: In another bowl, mix together the pumpkin puree, eggs, melted coconut oil, vanilla extract, and milk until smooth.
Combine Mixtures: Pour the wet ingredients into the dry ingredients and stir until just combined. Be careful not to overmix.
Fill Muffin Tin: Spoon about two-thirds of the muffin batter into each muffin cup. Add a dollop of the cream cheese filling on top of each batter portion. Then add more muffin batter on top to fill each cup about three-quarters full.
Bake: Bake in the preheated oven for about 20-25 minutes or until a toothpick inserted into the center comes out clean.
Cool and Serve: Allow the muffins to cool in the pan for about 10 minutes before transferring them to a wire rack to cool completely.
4. 3-Ingredient Pumpkin Cheesecake Muffins
Ingredients
- 1 (15 oz) can pumpkin puree
- 1 (15.25 oz) box spice cake mix (or yellow cake mix)
- 1 (8 oz) package cream cheese, softened
Instructions
Preheat the Oven: Preheat your oven to 350°F (175°C) and line a muffin tin with paper liners or grease it well.
Mix the Muffin Batter: In a large bowl, combine the pumpkin puree and the spice cake mix. Stir until well blended. This will create a thick batter.
Prepare the Cream Cheese Filling: In another bowl, beat the softened cream cheese until smooth. You can add a little sweetener or vanilla extract if desired, but it’s optional.
Fill the Muffin Tin: Spoon about 2 tablespoons of the pumpkin batter into each muffin cup. Add about 1 tablespoon of the cream cheese filling on top of the batter. Then, add another tablespoon of pumpkin batter on top to cover the cream cheese filling.
Bake: Bake in the preheated oven for about 20-25 minutes, or until a toothpick inserted into the center comes out clean.
Cool and Serve: Allow the muffins to cool in the pan for about 10 minutes before transferring them to a wire rack to cool completely.
5. Starbucks Pumpkin Cheesecake Muffin Recipe
Here’s a copycat recipe for Starbucks Pumpkin Cheesecake Muffins that captures the delicious flavors of the original:
Ingredients
For the Muffins:
- 1 ½ cups all-purpose flour
- ¾ cup granulated sugar
- 1 teaspoon baking powder
- 1 teaspoon baking soda
- ½ teaspoon salt
- 1 tablespoon pumpkin pie spice
- 1 cup pumpkin puree (not pumpkin pie filling)
- ¼ cup unsalted butter, melted
- 2 large eggs
- 1 teaspoon vanilla extract
For the Cream Cheese Filling:
- 8 oz cream cheese, softened
- ¼ cup granulated sugar
- ½ teaspoon vanilla extract
- 1 egg yolk
Instructions
Preheat the Oven: Preheat your oven to 350°F (175°C) and line a muffin tin with paper liners or grease it well.
Prepare the Cream Cheese Filling: In a medium bowl, beat the softened cream cheese, granulated sugar, vanilla extract, and egg yolk until smooth. Set aside.
Mix Dry Ingredients: In a large mixing bowl, combine the all-purpose flour, sugar, baking powder, baking soda, salt, and pumpkin pie spice. Whisk until well combined.
Combine Wet Ingredients: In another bowl, mix together the pumpkin puree, melted butter, eggs, and vanilla extract until smooth.
Combine Mixtures: Pour the wet ingredients into the dry ingredients and stir until just combined. Be careful not to overmix.
Fill Muffin Tin: Spoon about two-thirds of the muffin batter into each muffin cup. Add about a tablespoon of the cream cheese filling on top of each muffin batter portion. Then add more muffin batter on top to fill each cup about three-quarters full.
Bake: Bake in the preheated oven for about 18-20 minutes or until a toothpick inserted into the center comes out clean.
Cool and Serve: Allow the muffins to cool in the pan for about 10 minutes before transferring them to a wire rack to cool completely.
These muffins are moist, flavorful, and perfect for fall! Enjoy them as a delightful treat with your morning coffee or as an afternoon snack!
6. Low-Carb Pumpkin Cheesecake Muffin recipe
Here’s a Low-Carb Pumpkin Cheesecake Muffin recipe that combines the rich flavors of pumpkin and cheesecake while keeping it keto-friendly.
Ingredients
For the Muffins:
- 2 cups almond flour
- ½ cup granulated sweetener (like Swerve or erythritol)
- 1 teaspoon baking powder
- ½ teaspoon baking soda
- ½ teaspoon salt
- 1 teaspoon pumpkin pie spice (or a mix of cinnamon, nutmeg, and ginger)
- 1 cup pumpkin puree
- ¼ cup melted butter (or coconut oil)
- 2 large eggs
- 1 teaspoon vanilla extract
For the Cream Cheese Filling:
- 8 oz cream cheese, softened
- ¼ cup powdered sweetener (like Swerve or erythritol)
- 1 teaspoon vanilla extract
- 1 egg yolk
Instructions
Preheat the Oven: Preheat your oven to 350°F (175°C) and line a muffin tin with paper liners or grease it well.
Prepare the Cream Cheese Filling: In a medium bowl, beat the softened cream cheese, powdered sweetener, vanilla extract, and egg yolk until smooth. Set aside.
Mix Dry Ingredients: In a large mixing bowl, combine the almond flour, granulated sweetener, baking powder, baking soda, salt, and pumpkin pie spice. Whisk until well combined.
Combine Wet Ingredients: In another bowl, mix together the pumpkin puree, melted butter, eggs, and vanilla extract until smooth.
Combine Mixtures: Pour the wet ingredients into the dry ingredients and stir until just combined. Be careful not to overmix.
Fill Muffin Tin: Spoon about two-thirds of the muffin batter into each muffin cup. Add about a tablespoon of the cream cheese filling on top of each batter portion. Then add more muffin batter on top to fill each cup about three-quarters full.
Bake: Bake in the preheated oven for about 20-25 minutes or until a toothpick inserted into the center comes out clean.
Cool and Serve: Allow the muffins to cool in the pan for about 10 minutes before transferring them to a wire rack to cool completely.
These low-carb pumpkin cheesecake muffins are perfect for enjoying during fall while keeping your carb intake low! Each muffin is moist and flavorful with a delightful cheesecake center. Enjoy!
7. Vegan Pumpkin Cheesecake Muffins
Here’s a delicious recipe for Vegan Pumpkin Cheesecake Muffins.
Ingredients
For the Muffins:
- 1 ¾ cups all-purpose flour (or gluten-free flour blend)
- 1 ½ teaspoons baking soda
- 1 teaspoon baking powder
- 1 teaspoon pumpkin pie spice
- ½ teaspoon salt
- 1 cup pumpkin puree (not pumpkin pie filling)
- ½ cup granulated sugar
- ½ cup brown sugar
- ½ cup unsweetened applesauce
- ½ cup coconut oil (melted) or vegetable oil
- 2 teaspoons vanilla extract
- ⅓ cup unsweetened almond milk (or any plant-based milk)
For the Cream Cheese Filling:
- 8 oz vegan cream cheese (such as Kite Hill or Tofutti)
- ¼ cup granulated sugar (or powdered sugar)
- 1 teaspoon vanilla extract
Instructions
Preheat the Oven: Preheat your oven to 350°F (175°C) and line a muffin tin with paper liners or grease it well.
Prepare the Cream Cheese Filling: In a medium bowl, mix the softened vegan cream cheese, granulated sugar, and vanilla extract until smooth. Set aside.
Mix Dry Ingredients: In a large mixing bowl, whisk together the flour, baking soda, baking powder, pumpkin pie spice, and salt until well combined.
Combine Wet Ingredients: In another bowl, mix together the pumpkin puree, both sugars, applesauce, melted coconut oil, vanilla extract, and almond milk until smooth.
Combine Mixtures: Pour the wet ingredients into the dry ingredients and stir until just combined. Do not overmix.
Fill Muffin Tin: Spoon about two-thirds of the muffin batter into each muffin cup. Add about a tablespoon of the cream cheese filling on top of each muffin batter portion. Then add more muffin batter on top to fill each cup about three-quarters full.
Bake: Bake in the preheated oven for about 20-25 minutes or until a toothpick inserted into the center comes out clean.
Cool and Serve: Allow the muffins to cool in the pan for about 10 minutes before transferring them to a wire rack to cool completely.
