System and methods for facilitating the settlement of financial accounts across different entities utilize a host computer system that tracks financial transactions made at each merchant location or store and uses this information to reconcile accounts across different entities. In one embodiment, the host computer periodically performs a net settlement analysis of the transactional data received from each entity's stores. A request is prepared to transfer funds from each entity's bank account having a positive net settlement amount into a central entity bank account. A request is also prepared to transfer funds into each entity's bank account having a negative net settlement amount from the central entity bank account.