System and methods for managing third party tokens and transaction across issuer ecosystems are disclosed. In one embodiment, in an information processing device comprising at least one computer processor, a method for managing payment tokens may include: (1) a first computer program associated with a financial institution and executed by the information processing device accessing a payment token associated with a second computer program executed by the information processing device; (2) the first computer program identifying the payment token as associated with a financial instrument issued by the financial institution; (3) a backend for the financial institution generating an association between the payment token and the financial institution; and (4) the backend for the financial institution communicating the association to an authorization platform for the financial institution.