Research collaboration is key to faculty career success in science, technology, engineering, and mathematics (STEM). Yet little research has considered how faculty from multiply marginalized identity groups experience collaboration compared to colleagues from majority groups. The present study fills that gap by examining similarities and differences in collaboration experiences of faculty across multiple marginalized groups, and the role of department climate in those experiences. A survey of STEM faculty at a large public research university found that faculty from underrepresented groups – in terms of gender, race, and sexual orientation – had more negative experiences with department-level research collaborations. Moreover, faculty with multiply marginalized identities had worse collaboration experiences than others with a single marginalized identity or none. They also perceived their department climate to be less inclusive, equitable, and transparent; and felt their opinions were less valued in their department than colleagues from majority groups. Negative department climate, in turn, mediated and predicted less hospitable experiences with department-level research collaborations. These data suggest that multiply marginalized faculty, across different identity groups, share some common experiences of a “chilly” department climate relative to their peers from majority groups that impede opportunities for scientific collaboration, a key ingredient for faculty success. These findings have policy implications for retention of diverse faculty in university STEM departments.