Organisational change is associated with adverse health outcomes for employees. The association may be mediated by changes in the psychosocial work environment. Workplace social capital (WSC) is a recent construct, which has been shown predictive of health outcomes when studying the psychosocial work environment. Currently, there is no epidemiological evidence concerning the impact of organisational change on WSC. This study examines the impact of organisational change on WSC in public hospitals in Denmark. An open cohort-study of hospital employees in the Capital Region of Denmark provided longitudinal data on 1639 work units within 11 hospitals. WSC was assessed by employees during workplace evaluations in 2011 and 2014 (41.710 responses, 81% response rate). WSC was rated on 8 items using 5–7 point Likert-scales, and then transformed to a 0–100 scale. Exposure data were provided by work unit leaders, recollecting four types of organisational change from 2011 to 2014; mergers, layoffs, relocations and downsizing. A multilevel model was used to analyses the change of WSC-scores within each work unit. The model estimated the effect of organisational change and adjusted for changes in the size of the work unit and the vocation, age, gender and seniority of the employees. In work units exposed to one or more organisational changes in the three year period, WSC decreased by 1.5 points (95% CI: (−2.2; −0.7)). Mergers had the biggest impact, decreasing WSC by 1.9 points (95% CI: (−2.8; −1.0). Organisational changes adversely impacted the workplace social capital, possibly mediating the effect on employee health.