A memory coupled to a programmable logic device (PLD) is configured through the PLD's JTAG port. A soft core loaded into the PLD connects to the JTAG port and memory. An external programming host device connects to the JTAG port, sends instructions and data to and receives data from the memory via the JTAG port and soft core. A synchronization JTAG instruction is loaded, and a Shift Data state of the JTAG port state machine is used. The programming host device and soft core are synchronized, and a memory chip select is asserted. A memory instruction, such as READ, WRITE or ERASE is loaded into the memory. An RTI state of the state machine is used to wait for instruction completion and the chip select is deasserted. Another instruction is processed starting with using the Shift Data state. Alternatively, a PLD Shift Data Register is used in conjunction with the soft core.