Lean Manufacturing includes an ensemble of methods to analyze and continuously improve the functioning of manufacturing systems. The research presented in the literature highlights the fact that these methods are, on their own, in a process of continuous improvement as tools, being used in different ways, for different production systems. The paper presents an algorithm that facilitates the choice of the performance evaluation method, and the choice of the method of improvement that needs to be implemented for an efficient analysis and for a continuous increase of the manufacturing system performance. In addition to these, for the JobObservation and 5S methods, chartflows are proposed and specific tools are developed (questionnaires, forms etc.) that are meant to facilitate the implementation and to focus (guide) the user in the direction of improvement for the analyzed process. The algorithm, techniques, and tools developed in this research were used in a case study that took place in a production system “plastic injection”. Thus, a series of important improvements were made in the functioning of the production system, consisting of the reduction of production area, decrease of cycle time, decrease of the number of operators, stabilization, standardization, and securing of the work processes. All this has led to the improvement of several key performance indicators (KPIs) of the production system. The analysis of the investment in the reorganization of the production system in relation to the obtained gains shows a payback of approximately 1 month, proving the efficiency of use in such a form of the Lean Manufacturing methods.