Lean Six Sigma (LSS) is a data-driven philosophy that drives performance improvement by eliminating waste and reducing variability. Food Manufacturing (FM) companies introduce programs like LSS to improve competitiveness. However, LSS implementations are complicated and complex. Companies must carefully manage the implementation of LSS to achieve the desired outcomes. In line with this, proper management of Critical Success Factors (CSFs) can enhance the initiative’s chances of success. This research aims to identify, rank, and understand the CSFs, and recommend strategies to manage them within Philippine FM companies. A combined approach of structured literature review, structured survey, and structured interview were used to gather the necessary data. The thematic analysis and Relative Importance Index method revealed that there are 15 CSFs. These CSFs were synthesized into 4 clusters: Synergy, Expertise in LSS, Effective Management, and Dedicated Leadership. Thus, to be successful, all stakeholders within the company must have the essential hard and soft skills to execute the DMAIC framework and manage the initiative as a whole. More importantly, they must have the proper working environment, be aligned to the intended goal, and fully cooperate and contribute to the activities that must be accomplished to achieve the target future state.