Scholarly journals are often blamed for a gender gap in publication rates, but it is unclear whether peer review and editorial processes contribute to it. This article examines gender bias in peer review with data for 145 journals in various fields of research, including about 1.7 million authors and 740,000 referees. We reconstructed three possible sources of bias, i.e., the editorial selection of referees, referee recommendations, and editorial decisions, and examined all their possible relationships. Results showed that manuscripts written by women as solo authors or coauthored by women were treated even more favorably by referees and editors. Although there were some differences between fields of research, our findings suggest that peer review and editorial processes do not penalize manuscripts by women. However, increasing gender diversity in editorial teams and referee pools could help journals inform potential authors about their attention to these factors and so stimulate participation by women.