•A DSS based on a 3D fuzzy methodology has been developed.•The DSS allows to evaluate the level of alignment between an enterprise's knowledge and its KMSs.•The DSS proposes corrective actions and suggests strategies for KMS adoption to improve KM alignment.•The DSS is tested on a small and medium enterprise (SME) operating in the high-tech industry. The purpose of this paper is to propose a three-dimensional fuzzy logic approach to evaluate the level of alignment between the knowledge an enterprise possesses and the knowledge management systems (KMSs) it adopts. The study also aims to propose the KMSs best suited to reducing misalignment and improving operational performance in terms of efficiency and effectiveness, analysing the level of alignment between an enterprise's knowledge and its KMSs from both the ontological and epistemological points of view. The authors have used the proposed methodology to develop a software-based Knowledge Management Decision Support System (KM-DSS), which was tested on a small and medium enterprise (SME) operating in the high-tech industry. The results highlight that the proposed DSS allows managers to evaluate knowledge management processes and identify which KMSs to adopt to improve alignment with the nature of the knowledge their enterprise possesses as well as to increase their level of efficiency and effectiveness.