A method for performing a shuttle shift with a continuously variable transmission of a work machine is disclosed. The method may generally include adjusting a swash plate angle of a hydrostatic power unit of the transmission in a first direction to reduce a travel speed of the work machine in an off-going direction, initiating a directional swap between an off-going directional clutch of the continuously variable transmission and an on-coming directional clutch of the continuously variable transmission while the work machine is traveling in the off-going direction and adjusting the swash plate angle of the hydrostatic unit in a second direction after the initiation of the directional swap to reduce slippage across the on-coming directional clutch, wherein the second direction is opposite the first direction.