The purpose of this investigation is to emphasize the negative effects of security on transport performance. The methodology is based on the analysis of a large workshop with security experts and multiple case studies, where data is collected by means of observations, and unstructured and semi-structured interviews. The findings from the empirical data seem to demonstrate the initial hypothesis that security measures affect efficiency in terms of lower operational performance. Therefore, this paper discusses the importance of developing security capabilities to be integrated in existing logistics information systems. Only in this way will transport companies develop the capability to fully realize wins in terms of both security and efficiency.