The literature on the application of legal maternity protection measures in the workplace reveals that many organizations are failing to develop and maintain an in-house safety climate that manages to accommodate work and pregnancy. This study sought to understand managers’ and employees’ perceptions vis-à-vis different ways of managing pregnancy in healthcare settings. Further, the study aimed to identify pathways towards establishing a safety climate that makes pregnant employees feel protected and able to continue their work without discrimination or danger to their health or that of their unborn child. We investigated three healthcare institutions in Switzerland, carrying out 30 interviews with different stakeholders involved in maternity protection at work and analyzing their transcripts thematically. Managers and employees in the same healthcare institution can have divergent perceptions of maternity protection measures and their effects. Elements associated with pregnant employees perceiving a positive safety climate included their direct superiors’ perceived commitment to safety, shared perceptions of risks, the perception of adequate levels of information, the presence of an occupational health unit, and formal institutional procedures for managing and supporting pregnant employees. Incorporating and considering different stakeholders’ experiences is essential to understanding and improving the institution’s safety climate and women’s overall experience of pregnancy at work.