Systems and methods for managing library-based memory deduplication are disclosed. In one implementation, a processing device may start a first instance of an application on a host computer system. Responsive to detecting that the first instance completed an initialization stage, the processing device may create a data structure referencing a first plurality of memory pages created by the first instance of the application. The processing device may further identify, among a second plurality of memory pages associated with the application, a first memory page. The processing device may also identify, among the first plurality of memory pages referenced by the data structure, a second memory page identical to the first memory page. The processing device may further modify a pointer referencing the first memory page to reference the second memory page and may release the first memory page.