Methods and apparatus are disclosed for securely erasing partitions of reconfigurable logic devices such as FPGAs in a multi-tenant server environment. In one example, a method of securely erasing an FPGA includes identifying one partition of previously-programmed resources in the FPGA, erasing the identified partition by storing new values in memory or storage elements of the identified partition, and storing new values in memory or storage elements of additional external resources electrically connected to the integrated circuit and associated with the identified partition. Thus, other partitions and subsequent users of the identified partition are prevented from accessing the securely erased data. A configuration circuit, accessible by a host computer via DMA, can be programmed into the FPGA reconfigurable logic for performing the disclosed erasing operations.