Agile transformations cause fundamental changes to work designs. To better understand resistance to transformations, we shed light on employee preferences and the consequences of team and work organization changes for job satisfaction. We tested two hypotheses on how job satisfaction in agile transformations is influenced by a mismatch of perceived and preferred forms of organizing and a general preference for agile, hybrid, or more traditional forms of organizing. Therefore, we designed the self-stated preference method "pairwise comparison-based preference measurement". In summary, we identified team organization as the most important dimension in agile transformations. For requirements engineering, the distance between employee preferences and the perceived status quo was particularly large. Further, we found evidence that a larger distance between team and work organization preferences and perceptions negatively influenced job satisfaction. A relationship between a general preference for one form of organizing and job satisfaction was only weakly supported.