Methods and systems are providhed for controlling a sunshade associated with a sunroof system of a vehicle. In one embodiment, a method includes: determining, by a processor, a mode of the sunshade to be at least one of a linked mode and an unlinked mode; and selectively controlling, by a processor, a position of the sunshade based on one of a requested position of the sunshade and a requested position of a sunroof window, wherein the selectively is based on the mode.