A clock domain separation device and a method for operating the device is provided for separating two clock domains of a bus system in a system-on-chip (SoC). The clock domain separation device is a hardware module that acts as a guarding between the two clock domains that contain either bus end, and is generally applicable with handshake-type bus protocols. The clock domain separation module allows for each clock domain to switch its clock on and off independently from the state of the other clock domains, without risking data loss or protocol violation.