The food manufacturing industry, especially small and medium-sized enterprises (SMEs), faces critical challenges related to operational inefficiencies and machine availability. Previous research has highlighted the need for Lean Manufacturing tools like 5S, SMED, and Total Productive Maintenance (TPM) to address these issues. This study aimed to improve equipment availability and reduce downtimes in a food processing SME in Peru, focusing on optimizing production through these methodologies. The proposed solution involved the application of Lean tools to restructure workplace organization, streamline machine setup times, and implement autonomous maintenance practices. Key findings demonstrated a significant improvement, with equipment availability increasing from 77.01% to 82%, and a reduction in setup times by 30.81%. The study’s contribution is both academic and practical, providing a replicable model for similar SMEs in the food industry. Future research should explore further adaptations of Lean-TPM frameworks to enhance sustainability and long-term operational performance across various sectors.