Although the Theory of Constraints (TOC) is a widely known management concept, it warrants further research, particularly in terms of its application. The study investigates TOC implementation in a medium-scale manufacturing system with diverse products. The instrumental case study methodology is employed in this study, and the conceptual studies assess the case. The study helps to elucidate the methodology of TOC implementation in a manufacturing system. Instead of the five-step sequential approach that exploits constraints one after another, the cycles of system productivity target points are proposed, where each improvement cycle simultaneously considers several constraints. The proposed methodology is visualised, several implications and suggestions for constraint identification are provided, and a new method of bottleneck identification is elaborated in this study.