Operational efficiency in Peruvian chocolate SMEs remains limited despite a sector benchmark approaching 75%. Artisanal plants continue to face recurring failures such as thermal variability during tempering, inaccurate filling of buffer tanks, reprocessing in molding, and excessive changeover times that compromise product quality and restrict productive capacity. The plant analyzed in this study operates at only 39.28% real efficiency, evidencing structural gaps in flow synchronization, standardization, and control of critical variables. The main contribution of this research is the formulation of a low-cost, high-impact Lean improvement model specifically tailored to artisanal chocolate manufacturing, addressing a methodological gap in the literature that traditionally focuses on highly automated plants. This integrated model combines SMED, Poka-Yoke, and Jidoka-based continuous flow to reduce operational variability and enhance process stability in low-automation environments. The model was subsequently validated through time–motion studies, pilot testing, and discrete-event simulation with 30 replicates per scenario, confirming substantial improvements: transfer time reduction (180 to 44 min), decreased tank-level variability (20% to 5.5%), reduced reprocessing (25% to 5%), and an increase in overall efficiency to 75%.