Editorial decision-making is a fundamental element of the scientific enterprise. We examined whether contributions to editorial decisions at various stages of the publication process is subject to gender disparity, based on analytics collected by the biomedical researcher-led journal eLife. Despite efforts to increase women representation, the board of reviewing editors (BRE) was men-dominant (69%). Moreover, authors suggested more men from the BRE pool, even after correcting for men’s numerical over-representation. Although women editors were proportionally involved in the initial editorial process, they were under-engaged in editorial activities involving reviewers and authors. Additionally, converging evidence showed gender homophily in manuscripts assignment, such that men Senior Editors over-engaged men Reviewing Editors. This tendency was stronger in more gender-balanced scientific disciplines. Together, our findings confirm that gender disparities exist along the editorial process and suggest that merely increasing the proportion of women might not be sufficient to eliminate this bias.