The correct design of leakage inductances for multi-winding transformers can be challenging due to the fact that all the windings are interacting. This parameter plays a major role in the operation in isolated power converters such as dual active bridge or multiple active bridge power converters. The existing analytical and numerical methods of estimation of the mentioned leakage inductances are limited in accuracy and do not allow to simultaneously design the device according to the required parameters, as well as to predict the value of leakage inductance. In this paper, a comprehensive methodology has been developed for the design of a multi-winding transformer with accurate leakage inductance determination during the design process. Within the methodology, several stages are proposed: analytical, numerical, validation and prototyping. Each of the stages allows to accurately determine the leakage inductance and to achieve the best possible fabrication quality of the prototype device.