This study examines the influence of organizational structures—functional, divisional, matrix, and flat—on the implementation and outcomes of lean manufacturing within small and medium-sized manufacturing enterprises (SMEs). Using a mixed-methods approach, data were collected from five SMEs over a five-year period, involving 17 lean projects, more than 100 employees, and multiple case studies supported by interviews, focus groups, and surveys. Performance indicators such as revenue growth, return on investment (ROI), cycle time reduction, and employee perceptions were compared across structures. Findings reveal that organizational structure significantly shapes lean implementation outcomes. Matrix organizations achieved the highest mean revenue increase (53.5%) and cycle time reduction (66%), highlighting their adaptability. Flat organizations reported the strongest ROI (243.3%) and the greatest reduction in customer complaints (63.3%), reflecting the benefits of reduced hierarchy and quicker decision-making. Functional organizations demonstrated strengths in process reliability, achieving the highest on-time delivery (96%) and the lowest scrap rate (1.55%), while divisional organizations consistently underperformed, with the lowest mean scores across revenue (20.4%), customer complaint reduction (23.8%), and communication effectiveness (3.03/5). Qualitative analysis underscored common challenges, including resistance to change and decision-making delays, mitigated through leadership support, training, and cross-functional collaboration. Sentiment analysis showed that while divisional structures remained largely neutral, flat and matrix organizations experienced significant positive shifts in employee acceptance after 10 weeks. This research highlights that no single structure guarantees success; instead, aligning lean initiatives with organizational dynamics is critical. The findings provide managers with evidence-based insights to tailor lean strategies, enhance employee engagement, and maximize operational efficiency in SMEs.