Modern agriculture is undergoing a paradigm shift toward eco-friendly methodologies that enhance seed material quality while minimizing chemical inputs. This study evaluates the impact of Effective Microorganism (EM) exposure (variants E1 and E2) on the morpho-physiological parameters and phytosanitary health of potato tubers. The primary objective was to determine the efficacy of microbial priming in suppressing the infection rates of Streptomyces scabies (common scab) and Rhizoctonia solani (black scurf) across 14 genetically diverse cultivars. A three-year field experiment (2019–2021) was conducted using a split-plot design with three replications. The study analyzed the interaction between EM exposure times and the genetic resistance potential of the selected cultivars. Statistical analysis confirmed that pre-planting microbial treatments significantly inhibited pathogen development. EM applications (E1 and E2) reduced the infection rates of both S. scabies and R. solani through an “escape mechanism,” whereby treated tubers exhibited accelerated biomass accumulation and reached physiological maturity before peak pathogen pressure. Furthermore, treatments optimized the physiological state and vigor of the tubers, establishing a robust physiological barrier against soil-borne infections. The application of EMs proves to be a highly effective, non-invasive biostimulation method. A significant difference was observed in the responding varieties between EM treatments and the cultivars innate genetic resistance, particularly in cultivars with higher baseline resistance. The use of EM biostimulants significantly modifies the health of tubers, and the direction of these changes is strictly determined by the variety factors. The results suggest that microbial priming not only enhances plant growth kinetics but also induces systemic resistance, offering a viable ecological alternative to traditional chemical seed dressings in sustainable potato production.