This work proposes the design of an autonomous system to monitor the biological transformation of inert regolith into a functionally fertile substrate through controlled bacterial inoculation, with implementation at the Mars Desert Research Station (MDRS), Utah, during the Team Peru VI mission. The research addresses food autonomy in long-duration space missions through In-Situ Resource Utilization (ISRU), integrating applied bioengineering with autonomous mechatronic systems. The approach employs a bacterial consortium selected for its ability to induce biogeochemical processes, fix atmospheric nitrogen, and improve substrate structure through exopolysaccharide production. The biological process will be supported by an ESP32-based system to monitor substrate pH, electrical conductivity, temperature, and moisture at 15-minute intervals, while also providing automated irrigation control. The study aims to demonstrate that integrating biological processes with embedded systems can enable the identification of early indicators of substrate transformation during a 14-day mission, while reducing crew operational workload, human error in data acquisition, and water consumption. Validation under the highly arid conditions of the MDRS will allow assessment of system robustness and applicability to Mars analog environments. The convergence of applied microbiology and automation seeks to establish a scalable technological foundation for future autonomous agricultural systems and smart greenhouses on Mars. Additionally, the proposed methodology could be transferable to the restoration of degraded soils in Latin America, contributing to agricultural resilience, arid-land management, and food security.