In a medium bowl, beat the softened cream cheese until smooth.
Add the granulated sugar and vanilla extract; mix until well combined.
Stir in the all-purpose flour until fully incorporated.
Cover the mixture and refrigerate while preparing the cookie dough.
Prepare the Cookie Dough:
In a medium bowl, whisk together the all-purpose flour, baking soda, and salt.
In a large bowl, using an electric mixer, beat the softened butter and cream cheese until smooth and creamy.
Add the granulated sugar and light brown sugar; beat until light and fluffy.
Mix in the egg and vanilla extract until fully incorporated.
Gradually add the dry ingredients to the wet mixture, mixing until just combined.
Fold in the semi-sweet chocolate chips.
Cover the dough and refrigerate for at least 30 minutes to 1 hour.
Assemble and Bake:
Preheat the oven to 350°F (175°C). Line baking sheets with parchment paper or silicone baking mats.
Using a cookie scoop or tablespoon, scoop approximately 1½ tablespoons of cookie dough and flatten it slightly.
Place about 1 teaspoon of the chilled cheesecake filling in the center of the flattened dough.
Top with another 1½ tablespoons of flattened cookie dough, sealing the edges to encase the cheesecake filling.
Place the stuffed cookie dough balls onto the prepared baking sheets, spacing them about 2 inches apart.
Bake for 9-11 minutes, or until the edges are set and slightly golden. The centers may appear slightly undercooked but will firm up as they cool.
Remove from the oven and let the cookies cool on the baking sheet for 5 minutes before transferring them to a wire rack to cool completely.
Notes
Storage: Store the cookies in an airtight container in the refrigerator for up to 5 days. For the best taste, allow them to come to room temperature before serving.
Freezing: These cookies can be frozen. Place baked and cooled cookies in a single layer on a baking sheet to freeze, then transfer to a freezer-safe bag or container. Thaw in the refrigerator overnight before enjoying.
Variations: Feel free to experiment by adding mix-ins such as nuts or using different types of chocolate chips to suit your preferences.