As an important part of China’s green manufacturing systems, green factory certification is a vital tool to accelerate green transformation in the industries sector. Based on national-level data on green factory certification, this study systematically examines the impact mechanism and economic consequences of green factory certificationon firms’ environmental protection investment from the perspective of peer effects. The research reveals that green factory certification exhibits significant peer effects, wherein the environmental protection investment of non-certified firms is increased by the presence of green factory certified firms within the same region and industry. The conclusion remains valid after a series of robustness and endogeneity tests. Moreover, the peer effects of green factory certificationon is stronger in the sample of large-scale firms, non-state-owned firms, heavily polluting firms, and non-high-tech firms. Furthermore, the study indicates that, compared to governance-oriented environmental protection investment, the effects of green factory certification have a more pronounced promoting effect on prevention-based environmental protection investment. Finally, this study discovers new evidence that green factory certification can promote firms’green innovation performance and regional environmental performance through peer effects. This study provides empirical evidence assessing the effectiveness of green factory certification as a leading exemplar, and offers practical insights from the perspective of peer effects to encourage firms to achieve green transformation.