Objective Allostatic Load (AL) represents the strain on the body produced by repeated physiologic or allostatic responses activated during stressful situations. Several cross-sectional studies have found empirical substantiation for the relationship between impaired psychosocial work environment and high AL. The aim of this longitudinal study is to investigate changes in AL during workplace reorganization that has been shown to cause impaired psychosocial work environment. Moreover, we aim to investigate the association between changes in AL and changes in psychosocial work environment (job strain, effort-reward imbalance) and psychological distress (stress symptoms and perceived stress). Methods A major reorganization of non-state public offices was effectuated in Denmark on 1 January 2007. In 2006 and 2008, we collected clinical and questionnaire data from 359 participants, 265 women and 94 men, employed in seven municipality or county administrations. Four municipalities and one county merged with others, while one municipality and one county remained unmerged. We calculated the AL score based on 13 physiological markers reflecting stress responses of the cardiovascular, metabolic, neuroendocrine and immune systems. We analysed changes in AL from 2006 to 2008. Results AL increased significantly during workplace reorganization in the whole study group but we observed only a tendency of significant increase in AL in the merger group compared with the control group. Moreover, we observed no association between the changes in AL and changes in psychosocial work environment and psychological distress. Conclusions This result leaves the conclusion unclear but contributes to the limited research in this area with a longitudinal design and focus on low-risk levels and small changes in AL in healthy people as predictor of future disease.