Introduction Clinical reasoning (CR) among healthcare professionals working in emergency medical services (EMS) who focus on ambulance care is a vital part of ensuring timely and safe patient care. The EMS environment continually fluctuates, so clinicians constantly need to adapt to new situations. Organizational support is described as important for CR, but overall, research on organizational influences for CR in an EMS context is lacking. An increased understanding of these influencing factors can assist in the development of EMS by strengthening CR among clinicians. Therefore, the purpose of this study was to investigate the organizational factors influencing EMS clinicians’ CR. Methods Using a qualitative single case study design, an EMS organization in southwestern Sweden was explored. Data were collected from participant observations of patient encounters, individual and group interviews with clinicians and organizational representatives, and organizational document audits. Data were analyzed using qualitative content analysis and triangulation of data sources. Results The results revealed several organizational influencing factors. Collaboration and information sharing internally and externally were emphasized as essential components influencing CR. Additionally, the structure for the clinicians’ ‘room for action’ appeared confused and created uncertainties for CR related to decision mandates. Conclusion The conclusion is that organizational factors do play an important role in clinicians’ CR. Moreover, the EMS community needs to develop suitable forums for discussing and developing these influencing factors across organizational hierarchies. Finally, clarification is needed on clinicians’ ‘room for action’ within their own organization but also with possible collaborators.