The agro-industrial quinoa sector in Peru shows operational efficiency levels below 85%, largely affected by high reprocessing, grain breakage, and variability in microbiological quality during storage. Although Lean and Total Productive Maintenance (TPM) have demonstrated benefits in agro-industrial environments, their integration with inventory-rotation methods such as the First Expired, First Out (FEFO) approach remains limited—particularly in processes where microbiological stability is critical. This study proposes an integrated improvement model for quinoa-exporting companies, combining FEFO-based inventory management, Standardized Work (SW), and TPM to intervene in critical stages of the production flow. Validation followed a hybrid approach: FEFO and SW were evaluated through pilot implementation using real production cycles and cross-checked operational records, while TPM was validated through an Arena simulation model parameterized with plant data and tested across multiple replications to ensure statistical consistency. This multi-method validation strengthens the robustness of the findings and reduces the likelihood that improvements result from random process variation. The integrated model substantially reduced reprocessing, improved operational consistency, and stabilized equipment performance, offering a scalable and replicable framework for enhancing efficiency, minimizing waste, and ensuring quality control in food industries handling short-shelf-life products.