Small and medium-sized enterprises (SMEs) in Peru’s food sector face persistent profitability constraints arising from inefficient planning, elevated inventory costs, and unbalanced production processes. This study proposes an integrated improvement model that combines Material Requirements Planning (MRP), Heijunka (production leveling), and Systematic Layout Planning (SLP) in a gluten-free bakery SME. Empirical data from 2022 to 2024 reveal that labor accounted for 49.9% of total costs, the average production time per batch (24 jars) was 2.0 hours, and the unit fill rate reached only 39.3%, highlighting substantial operational inefficiencies. The proposed model is designed to improve inventory management through MRP, enhance labor efficiency via Heijunka, and shorten production cycles by implementing SLP. Validation conducted with Arena-based discrete-event simulation projects significant improvements in fill rate, production time per batch, labor cost share, and gross margin, consistent with industry benchmarks. Specifically, the analysis forecasts an increase of up to 18 percentage points in gross margin and an improvement of up to 50 percentage points in unit fill rate. Overall, the findings demonstrate the feasibility of integrating these tools in resource-constrained SMEs, thereby strengthening competitiveness and supporting sustainable growth in the food sector