This disclosure relates to methods and systems for dynamically partitioning of PCIe disk arrays based on software configuration/policy distribution. In one embodiment, at least one PCIe switch has an input port operatively connected to a respective CPU and at least one output port. A multiplexer is connected between the output port(s) of the at least one PCIe switch and a PCIe disk array, for example an NVMe SSD, and is configured to connect the PCIe disk array in a first configuration to a single PCIe switch in either one-x4 port or two x2 port mode, or in a second configuration to two PCIe switches in x2 port mode. The multiplexer can dynamically switch between the first configuration and the second configuration on the fly. Switching can occur, for example, in response to a hot-swap of an NVMe SSD or a policy change.