The seed industry plays a crucial role in global food production but it faces a persistent challenge in ensuring the health and quality of seeds, particularly those of tomato and pepper seeds, which represent key seed commodities on the global market. Seeds can serve as potential pathways for the introduction and dissemination of seed-borne bacteria, which may have devastating effects on crop yield, farmers’ remunerability, and food security. Therefore, fungicides and other antimicrobial compounds are extensively used to disinfect the seeds, thus increasing the input of chemicals in the agri-environment. In this review, we address aspects that connect disease epidemiology with seed infection and health, including seed contamination, endophytic colonization, and seed-borne infections. We focused on the main bacterial diseases affecting tomato and pepper seeds by discussing their official seed testing methods as requirements supporting a smooth seed trade. Moreover, we present a survey on the past and recent innovations for seed treatments, focusing on sustainable disinfection methods. Therefore, this review will be a short but indispensable guide for seed technologists and pathologists involved in the production of high-quality seeds, providing indications and suggestions to contrast seed-borne pathogen dissemination and avoid international controversies and complaints by phytosanitary authorities, extension services, and farmers.