A first method of protecting an engine and a transmission of a marine vessel during gear shifts and a second method of programming one or more Shift Protection Sequences (SPS) are disclosed. The first method includes receiving a Shift Request (SR) and activating a SPS from among a plurality of enabled SPS. The second method includes configuring a Shift Protection Type (SPT); enabling and configuring a plurality of required and SPS variables; and, optionally, enabling and configuring a plurality of optional SPS variables. The SPT may be a Basic Shift Protection (BSP), which includes time-based SPS; or the SPT may be an Advanced Shift Protection (ASP), which includes alternate time-based and operating-variable based SPS. The SPS of the ASP may be incrementally programmed and added to the BSP.