Seed deterioration induces the formation of free radicals and proliferation of microorganisms, but the application of external antioxidants may lessen these effects. The aim of this study was to investigate the antioxidant and antimicrobial activity of cathode and anode water on the physiological quality and health of Coffea arabica L. seeds. Part of the seeds were soaked in cathode water and the other part in anode water for periods of 1, 6, 12, 24, and 36 hours. The physiological quality of the seeds was evaluated by the germination test and tetrazolium test, and seed health by the Blotter test. Analysis of variance and Pearson correlation analysis were performed on the data for all the response variables. Soaking in cathode water or anode water up to 24 hours improves the physiological quality of coffee seeds. Anode water has a beneficial effect on the health of coffee seeds, reducing the incidence of Fusarium spp., Penicillium spp., Cladosporium spp., and Alternaria spp. after one hour of soaking and of Aspergillus spp. after six hours. Soaking in cathode water for a period of one hour leads to a reduction in the fungi Aspergillus spp., Fusarium spp., Cladosporium spp., and Alternaria spp., and reduction in Penicillium spp. after six hours.