Symbioses have shaped the evolution of life, most notably through the fixation of heritable symbionts into organelles. The inheritance of symbionts promotes mutualism and fixation by coupling partner fitness. However, conflicts arise if symbionts are transmitted through only one sex and can shift host resources toward the sex through which they propagate. Such reproductive manipulators have been documented in animals with separate sexes but not in other phyla or sexual systems. Here we investigated whether the investment in male relative to female reproduction differed between hermaphroditic host plants with versus without a maternally inherited fungal symbiont. Plants with the fungus produced more seeds and less pollen than plants lacking the fungus, resulting in an ∼40% shift in functional gender and a switch from male-biased to female-biased sex allocation. Given the ubiquity of endophytes in plants, reproductive manipulators of hermaphrodites may be widespread in nature.