Methods and systems for resolving clock management issues in emulation of a target system on a host system are disclosed. A first set of code instructions of a target program is interpreted to generate interpreted code instructions that emulate a first component on the host system. A second set of code instructions is translated to generate translated code instructions that emulate a second component of the target system on the host system. The interpreted instructions, are executed based on a first clock (which may be a fixed clock) and the translated instructions are executed based on a second clock (which may be a variable clock). The host system adjusts the first or second clock, execution of the translated or interpreted instructions or a memory access to maintain a desired synchronization between the translated instructions and the interpreted instructions.