Method and apparatus for encoding configuration data is described. An integrated circuit device having a configuration interface is coupled to boot memory coupled at the configuration interface. The boot memory contains boot cores for configuring the integrated circuit device via the configuration interface. The boot cores include a configuration encoder core and an internal processor interface core. The boot cores may further include a processor core. The configuration encoder core provides a peripheral interface internal to the integrated circuit device, and the boot memory contains at least one set of instructions for encoding configuration data read from configuration memory. The encoded configuration data may be sent via the peripheral interface. Alternatively, configuration encoder core may include a configuration bitstream for instantiating an encoder in configurable resources for encoding readback configuration data.