Here is my favorite pumpkin Greek yogurt cheesecake recipe, with a simple graham cracker crust, and a creamy filling made with pumpkin puree, Greek yogurt, light cream cheese, and warm fall spices.
This cheesecake has become my go-to dessert when I want something that feels indulgent but is actually lighter than traditional cheesecake. The Greek yogurt gives it such a nice tangy flavor that balances out the sweetness, and everyone always asks for seconds.
Why You’ll Love This Pumpkin Greek Yogurt Cheesecake
- Lighter than traditional cheesecake – Using Greek yogurt and light cream cheese means you get all the creamy, indulgent taste without the heavy guilt that usually comes with dessert.
- Perfect fall flavors – The pumpkin puree combined with warm spices like cinnamon, cloves, and nutmeg gives you that cozy autumn taste in every bite.
- Simple ingredients – You probably have most of these pantry staples on hand already, making this an easy dessert to whip up without a special grocery run.
- Ready in under 2 hours – From start to finish, this cheesecake comes together quickly for a homemade dessert that’s perfect for weeknight treats or last-minute entertaining.
What Kind of Pumpkin Puree Should I Use?
For this cheesecake, you’ll want to grab plain pumpkin puree from the baking aisle, not pumpkin pie filling. The difference is important – pumpkin pie filling already has sugar and spices added to it, which will throw off the balance of your recipe. Look for a can that says “100% pure pumpkin” on the label. Both canned and homemade pumpkin puree work great here, just make sure it’s at room temperature before you start mixing. If your puree seems watery, you can strain it through a fine-mesh sieve or cheesecloth for about 15 minutes to remove excess moisture and get a creamier cheesecake.
Options for Substitutions
This cheesecake is pretty forgiving when it comes to swaps, so here are some options that work well:
- Light cream cheese: You can use full-fat cream cheese if that’s what you have. The texture will be a bit richer and creamier, but it’ll still taste great.
- Greek yogurt: Regular yogurt works fine, though the cheesecake might be slightly less thick. You can also use sour cream for a tangier flavor – just use the same amount.
- Pumpkin puree: Make sure you’re using plain pumpkin puree and not pumpkin pie filling, as the filling already has sugar and spices added. If you can’t find pumpkin, sweet potato puree is a solid alternative.
- Spices: Don’t have all three spices? You can use 2 teaspoons of pumpkin pie spice instead of the cinnamon, cloves, and nutmeg combo.
- Graham cracker crumbs: Vanilla wafer cookies, digestive biscuits, or even gingersnaps make tasty crust alternatives. Just crush them up to get the same amount of crumbs.
- Sugar: You can swap white sugar with coconut sugar or brown sugar for a deeper, more caramel-like sweetness.
Watch Out for These Mistakes While Baking
The biggest mistake when making this cheesecake is using cold ingredients, which leads to lumps in your batter and an uneven texture – make sure your cream cheese, yogurt, pumpkin puree, and egg sit at room temperature for at least 30 minutes before mixing.
Overbaking is another common issue that causes cracks on the surface, so pull the cheesecake from the oven when the edges are set but the center still has a slight jiggle (it will firm up as it cools).
Don’t skip packing your graham cracker crust firmly into the pan with the bottom of a measuring cup, as a loose crust will crumble when you try to slice the cheesecake.
For the smoothest filling, mix on low speed and avoid overbeating once you add the egg, since too much air creates bubbles that can turn into cracks during baking.
What to Serve With Pumpkin Greek Yogurt Cheesecake?
This cheesecake is pretty rich on its own, so I like to keep things simple and serve it with a dollop of whipped cream and a sprinkle of extra cinnamon on top. A hot cup of coffee or spiced chai tea makes a great pairing since the warm spices in the drink complement the pumpkin and cinnamon flavors. If you want to add a little crunch, try serving it with some candied pecans or walnuts on the side, or even drizzle some caramel sauce over each slice for an extra treat. For a fall gathering, I’ll sometimes put out a bowl of fresh whipped cream and let everyone add their own toppings.
Storage Instructions
Store: Keep your pumpkin cheesecake covered in the fridge for up to 5 days. I actually think it tastes even better the next day after all the flavors have had time to meld together. Just cover it tightly with plastic wrap or aluminum foil to keep it from drying out.
Freeze: This cheesecake freezes really well if you want to make it ahead for the holidays. Wrap individual slices in plastic wrap and then place them in a freezer bag for up to 2 months. You can also freeze the whole thing if you prefer.
Serve: Let frozen slices thaw in the fridge overnight for the best texture. If you’re in a hurry, you can leave them at room temperature for about 30 minutes. The cheesecake is delicious cold straight from the fridge, or you can let it sit out for 10 minutes to take the chill off.
| Preparation Time | 15-20 minutes |
| Cooking Time | 25 minutes |
| Total Time | 100-125 minutes |
| Level of Difficulty | Medium |
Estimated Nutrition
Estimated nutrition for the whole recipe (without optional ingredients):
- Calories: 950-1100
- Protein: 13-18 g
- Fat: 48-55 g
- Carbohydrates: 120-135 g
Ingredients
For the crust:
- 3/4 cup graham cracker crumbs (I use Honey Maid)
- 1 tbsp sugar
- 3 tbsp butter (melted and cooled slightly)
For the cheesecake filling:
- 1 tsp vanilla extract
- 1 cup pumpkin puree (I use Libby’s)
- 1 tsp cinnamon (freshly ground preferred for more flavor)
- 4 oz light cream cheese (room temperature for smooth mixing)
- 1 egg (room temperature)
- 1/2 cup Greek yogurt (non-fat or 2% works well)
- 1/3 cup sugar
- 1/4 tsp nutmeg
- 1/4 tsp cloves
Step 1: Prepare the Crust Mixture
- 1 tbsp sugar
- 3 tbsp butter
- 3/4 cup graham cracker crumbs
Melt the butter in a small bowl and let it cool slightly for about a minute.
In another bowl, combine the graham cracker crumbs with 1 tablespoon of sugar, then pour the melted butter over and stir until the mixture resembles wet sand with a texture that holds together when pressed.
Set aside—this is your crust base that will provide a nice textural contrast to the creamy filling.
Step 2: Make the Pumpkin Cheesecake Filling
- 1 cup pumpkin puree
- 1 tsp cinnamon
- 4 oz light cream cheese
- 1 egg
- 1/2 cup Greek yogurt
- 1/3 cup sugar
- 1/4 tsp nutmeg
- 1/4 tsp cloves
- 1 tsp vanilla extract
In a medium bowl, combine the room-temperature cream cheese, pumpkin puree, Greek yogurt, 1/3 cup sugar, vanilla extract, cinnamon, nutmeg, and cloves.
Beat with an electric mixer on medium speed for about 2 minutes until the mixture is smooth and well combined with no lumps.
I like using freshly ground cinnamon here—it makes a noticeable difference in the flavor depth compared to pre-ground.
Once the mixture is smooth, gently fold in the egg just until incorporated, being careful not to overmix.
Step 3: Prepare Pan and Layer the Filling
- crust mixture from Step 1
- pumpkin cheesecake filling from Step 2
Preheat your oven to 350°F and line a muffin tin with paper liners.
Spoon approximately 1 tablespoon of the crust mixture from Step 1 into the bottom of each liner, pressing it down gently with the back of a spoon to create an even base.
Top each crust with 1.5 to 2 tablespoons of the pumpkin cheesecake filling from Step 2, filling each liner about three-quarters full.
I find that slightly overfilling gives you a more generous treat, and the filling doesn’t overflow during baking.
Step 4: Bake the Cheesecakes
Place the muffin tin in the preheated 350°F oven and bake for 25 minutes.
The cheesecakes are done when the tops are set but the centers still have a slight jiggle when you gently shake the pan—this ensures they stay creamy rather than becoming dry.
Remove from the oven and allow them to cool in the tin for about 1 hour at room temperature.
Step 5: Chill and Set
Once the cheesecakes have cooled to room temperature, transfer the muffin tin to the refrigerator and chill for at least 2 hours.
This resting time allows the flavors to meld and the texture to set properly.
You can make these up to 2 days ahead—store them in an airtight container in the fridge and they’ll actually taste even better as the flavors develop.
Perfect Pumpkin Greek Yogurt Cheesecake
Ingredients
For the crust:
- 3/4 cup graham cracker crumbs (I use Honey Maid)
- 1 tbsp sugar
- 3 tbsp butter (melted and cooled slightly)
For the cheesecake filling:
- 1 tsp vanilla extract
- 1 cup pumpkin puree (I use Libby's)
- 1 tsp cinnamon (freshly ground preferred for more flavor)
- 4 oz light cream cheese (room temperature for smooth mixing)
- 1 egg (room temperature)
- 1/2 cup Greek yogurt (non-fat or 2% works well)
- 1/3 cup sugar
- 1/4 tsp nutmeg
- 1/4 tsp cloves
Instructions
- Melt the butter in a small bowl and let it cool slightly for about a minute. In another bowl, combine the graham cracker crumbs with 1 tablespoon of sugar, then pour the melted butter over and stir until the mixture resembles wet sand with a texture that holds together when pressed. Set aside—this is your crust base that will provide a nice textural contrast to the creamy filling.
- In a medium bowl, combine the room-temperature cream cheese, pumpkin puree, Greek yogurt, 1/3 cup sugar, vanilla extract, cinnamon, nutmeg, and cloves. Beat with an electric mixer on medium speed for about 2 minutes until the mixture is smooth and well combined with no lumps. I like using freshly ground cinnamon here—it makes a noticeable difference in the flavor depth compared to pre-ground. Once the mixture is smooth, gently fold in the egg just until incorporated, being careful not to overmix.
- Preheat your oven to 350°F and line a muffin tin with paper liners. Spoon approximately 1 tablespoon of the crust mixture from Step 1 into the bottom of each liner, pressing it down gently with the back of a spoon to create an even base. Top each crust with 1.5 to 2 tablespoons of the pumpkin cheesecake filling from Step 2, filling each liner about three-quarters full. I find that slightly overfilling gives you a more generous treat, and the filling doesn't overflow during baking.
- Place the muffin tin in the preheated 350°F oven and bake for 25 minutes. The cheesecakes are done when the tops are set but the centers still have a slight jiggle when you gently shake the pan—this ensures they stay creamy rather than becoming dry. Remove from the oven and allow them to cool in the tin for about 1 hour at room temperature.
- Once the cheesecakes have cooled to room temperature, transfer the muffin tin to the refrigerator and chill for at least 2 hours. This resting time allows the flavors to meld and the texture to set properly. You can make these up to 2 days ahead—store them in an airtight container in the fridge and they'll actually taste even better as the flavors develop.
