The objective of the paper is to present the findings of the research on the application of mediation principles in solving organisational conflicts within the enterprise’s logistics system. Firstly, the interpretations of basic concepts are presented, i.e. the company’s logistics system, organisational conflict, the model of managing conflicts within the enterprise’s logistics system and mediation as well as the original concept of its principles (as the theoretical basis of the research). Secondly, the research methods are discussed, in particular the survey questionnaire, which was an essential tool for the empirical research. Thirdly, its results are summarised. Finally, the summary comprises conclusions from those studies, i.e. theoretical findings, practical recommendations and suggestions for the improvement of the suggested model of managing the considered conflicts. On the one hand, it has been found that both the scope of application of mediation principles to resolve the considered conflicts by managers within the analysed systems, and the level of mediation efficiency are satisfactory. On the other hand, in some cases, the scope of mediation can and should be expanded, and procedures and rules for its implementation should be developed. It is also desirable to provide training for managers to improve their mediation competences. It is also necessary to develop model solutions in the scope of methods and means of mediation based on broader comparative empirical research.