Ineffective plant layouts can account for 20–50% of total operating expenses, a challenge particularly acute for Small and Medium-sized Enterprises (SMEs) in developing nations where resources are limited. This study addresses these constraints by proposing an integrated, low-cost framework for layout redesign for a Bolivian paper manufacturer facing congestion and excessive transport distances. The methodology combines time studies, Discrete-Event Simulation (DES), Factory Physics, Systematic Layout Planning (SLP), and the Analytic Hierarchy Process (AHP) to diagnose and select optimal configurations. Two alternatives were obtained: (i) a machinery redistribution to minimize distance, and (ii) a layout integrating increased transport automation. Results demonstrate significant operational improvements. The first alternative increased throughput by 12.88%, reduced travel distance by 36.91%, and decreased WIP by 19.00%, while the second alternative increased throughput by 25.18%, reduced travel distance by 39.26%, decreased WIP by 29.25%, and improved cycle time by 8.00%. This research confirms that combining structured management tools offers a robust, transferable pathway to operational excellence without requiring complex algorithms or substantial capital investment.