Methods and systems for processing multi-stage programming (MSP) bits within one-time-programmable (OTP) memory are disclosed herein. Aspects of the method may comprise determining whether at least one MSP memory bit in the OTP memory is programmed and whether a register bit associated with said at least one MSP memory bit is asserted. If the register bit is deasserted and the MSP memory bit is unprogrammed, the MSP memory bit may be programmed. The register bit in the OTP memory may be associated with the MSP memory bit. The MSP memory bit may be programmed to logic zero or logic one. If the register bit associated with the MSP memory bit is asserted, programming of the MSP memory bit may be blocked. The register bit associated with the MSP memory bit may be reset and it may be determined whether the MSP memory bit is accessed.