Methods, systems, and apparatus, including computer programs encoded on computer storage media, for performing a partial reconfiguration of a partially reconfigurable programmable logic device. One of the methods includes providing, to an external memory device storing partial reconfiguration data, a first modified buffer offset. Before receiving partial reconfiguration data at the first modified buffer offset from the external memory, a first portion of prefetched data stored in local buffer memory is written to a configuration space of the partially reconfigurable device. When a first portion of data at the first modified buffer offset is received from the external memory device, the first portion of data at the first modified buffer offset is written to the configuration space of the partially reconfigurable device.