Sexual dimorphism is widespread among species with separate sexes and its extent is thought to be governed by the differential expression of thousands of genes between males and females (known as Sex-Biased Genes, hereafter SBGs). SBGs have been studied in numerous species, but rarely in a comparative way, which curtails our understanding of their evolution, especially during multiple independent transitions to separate sexes. We sequenced the transcriptomes of nine dioecious species, two gynodioecious species (separate females and hermaphrodites) and two hermaphrodite species from the Silene genus. Our dataset provides access to three independent transitions to dioecy (dating from less than 1 Myo to about 11 Myo). We demonstrated that male-biased expression emerges first during a transition to separate sexes, later followed by female-biased genes. Furthermore, we showed that, despite a mixture of selective regimes, positive selection significantly affects the evolution of some SBGs. Overall, this study provides new insights on the causes of SBG evolution during transitions to separate sexes. Teaser This study describes the evolution of sex-biased gene expression during a transition to separate sexes in plants.