As well as the large companies, also the small and medium-sized enterprises desire to take advantage of modern management methods to improve their process, their performances and competitiveness. The interest of the SMEs is focused on the elements of the Lean Six Sigma concept that seem to be appropriate to achieve these goals. As we have identified a gap in the research on this topic and a methodological gap about the LSS implementation in the small and medium companies, we propose a methodology that we called LSS Plutus to design, apply and control Lean Six Sigma in the SMEs. It is dedicated to the small and medium production enterprises and it takes into account their specificity. For this purpose, we have limited the traditional LSS toolbox used by the large companies. We have also created two variants to apply our methodology according to the different needs, capacities and maturities of the SMEs. We have developed indicators, tools, as well as a practical guide for applying the LSS for the production SMEs and its computerized version in TIBCO. To enhance the efficiency of the improvements, we have deployed the planning, standardization and sustainability of the changes. For this purpose, we propose to modify the criteria of the EFQM Excellence Model in order to adapt it to the operating conditions of the Lean Six Sigma method in the SMEs. The proposed methodology has been verified in two production SMEs in Poland and in France that confirmed its utility and effectiveness in terms of performance improvement and organizational development