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Make the crust: Take 2 pounds cream cheese out of their wrappers and let sit at room temperature while you prepare the crust, at least 30 minutes. Arrange a rack in the lower-middle position of the oven and heat the oven to 350°F.
Use your fingers to coat a small pat of butter all over the bottom and sides of a 9-inch or 10-inch springform pan. Cut 2 large pieces of aluminum foil (each about 18-inches long) and place them on a work surface on top of each other in a cross. Set the springform pan in the middle and fold the edges of the foil up and around the sides of the pan. The foil gives you extra protection against water getting into the pan during the water bath step.
If using whole graham crackers, process 12 rectangles in a food processor with the blade attachment (or in a ziptop plastic bag using a rolling pin) until they form fine crumbs, you should have 1 1/2 to 1 2/3 cups.
Place the graham cracker crumbs in a medium bowl. Melt 5 tablespoons unsalted butter in the microwave or on the stovetop, then stir this into the crumbs until they’re evenly moistened. Transfer the crumbs into the pan and use the bottom of a measuring cup to press it evenly into the bottom (not up the sides).
Place the crust in the oven (be careful not to tear the foil). Bake until the crust is fragrant and just starting to brown around the edges, 8 to 10 minutes. Meanwhile, place 1 1/2 cups pecans on a baking sheet and bake it at the same time until fragrant and lightly toasted, checking on them after 5 minutes. Let the crust cool on a wire rack until the sides of the pan are cool enough to comfortably touch before you prepare the filling, at least 20 minutes.
Make the filling: Place the cream cheese, 1 cup granulated sugar, 1 tablespoon cornstarch or 2 tablespoons flour, and 1/4 teaspoon kosher salt in the bowl of a stand mixer fitted with a paddle attachment. (Alternatively, use an electric handheld mixer and large bowl.) Mix on medium-low speed until the mixture is creamy like thick frosting and smooth, about 5 minutes. Scrape down the beater and the sides of the bowl with a spatula.
Add 1/2 cup sour cream and 1 teaspoon vanilla extract and beat on medium-low speed until combined and creamy. Scrape down the beater and sides of the bowl again. With the mixer on medium-low speed, beat in 3 large eggs and 1 large egg yolk one at a time. Wait until the previous egg is almost completely mixed into the batter before adding the next one.
Stir the whole batter a few times by hand, being sure to scrape the bottom of the bowl, to make sure everything is incorporated. The finished batter should be thick, creamy, and silky. Don't worry if you see a few specks of un-mixed cream cheese here and there; they will melt into the batter during baking and won't affect the finished cheesecake.
Place the pan in a roasting pan or other baking dish big enough to hold it. Bring about 8 cups of water to a boil and pour the water into the roasting pan so it goes about halfway up the sides of the springform pan, being careful not to splash any water onto the cheesecake. Carefully place the roasting pan in the oven.
Bake the cheesecake for 50 to 60 minutes. Cakes baked in a 10-inch pan will take 50 to 55 minutes; cakes in a 9-inch pan will take 55 to 60 minutes. The cheesecake is done when the outer 2 to 3 inches look slightly puffed and set, but the inner circle still jiggles (like Jell-O) when you gently shake the pan. Some spots of toasted golden color are fine, but if you see any cracks starting to form, move on to the next step right away.
Leave the cheesecake in the oven. Turn off the oven and crack the door open or prop it open with a wooden spoon. Let the cheesecake cool slowly for 1 hour.
Remove the cheesecake from the oven and from the water bath, unwrap the foil, and transfer it to a cooling rack. Run a thin-bladed knife around the edge of the cake to make sure it's not sticking to the sides (which can cause cracks as it cools). Let the cheesecake cool completely on the rack, about 1 1/2 hours.
Chill the cheesecake, uncovered, for at least 4 hours or up to 3 days in the refrigerator. This step is crucial for letting the cheesecake set and achieving perfect cheesecake texture — don't rush it.
Make the pecan pie topping: Coarsely chop about 1 cup of the toasted pecans, and leave the remaining 1/2 cup whole.
Place 6 tablespoons unsalted butter, 3/4 cup packed dark brown sugar, and 1/2 teaspoon kosher salt in a large saucepan over medium heat. Cook, whisking frequently, until the butter is completely melted and the mixture is completely smooth and bubbling all over, 6 to 8 minutes. Whisk in 1/2 cup heavy cream until completely combined and bubbling again.
Remove from the heat and stir in the chopped and whole pecans and 1/2 teaspoon vanilla extract. Set aside to cool to room temperature, 30 to 45 minutes.
Take the cheesecake out of the refrigerator and unmold it. You can serve the cake right from the bottom of the springform pan, or use a large off-set spatula to gently unstick the crust from the pan and transfer it to a serving platter. Spoon the pecan pie topping over the cheesecake before slicing.