The food manufacturing sector in Peru faces persistent challenges related to low productivity, operational variability, and resource waste, which restrict the competitiveness of SMEs. The sector represented 13.2% of national GDP in 2025 (Ministerio de la Producción, 2025), but despite its importance, many food-sector SMEs show limited adoption of Lean Manufacturing tools, relying on informal practices and lacking standardized processes. This study evaluates the implementation of 5S and standardized work in a food manufacturing SME producing snack-type products. The improvement effort focused on the main production line, which includes four products and four stages: mixing, kneading, cutting, and baking. The diagnostic phase identified workplace disorder and nonstandardized tasks as key drivers of rework, idle time, and productivity variability. Using Deming’s continuous improvement cycle (Plan–Do–Check–Act), productivity increased from 57.75 kg/USD to 69.53 kg/USD, waste decreased from 3% to 2.5%, and adherence to 5S improved from 30% to 78.22%. These results demonstrate the effectiveness of Lean tools in enhancing operational performance and highlight their potential to strengthen the competitiveness and sustainability of food-sector SMEs in Peru.