The coffee disease complex known as corky-root, composed of the root-knot nematode Meloidogyne arabicida and Fusarium oxysporum, causes serious damage to Coffea arabica in Costa Rica. Resistance to Meloidogyne arabicida alone and to the field population (M. arabicida, M. exigua, F. oxysporum) was evaluated under controlled and field conditions. The studied material consisted of subspontaneous-derived C. arabica accessions, C. canephora accessions, introgression lines derived from the interspecific Timor Hybrid (C. arabica x C. canephora) and F1 hybrids from crosses between subspontaneous-derived accessions and cultivars. Accessions resistant to M. arabicida and to the field population were identified at varying frequencies in the different groups of study materials. The results showed that resistance to corky-root is heritable and that genetic resistance to M. arabicida is an effective strategy against corky-root disease. By using C. canephora rootstocks, it was possible to substantially reduce mortality in the field and reduce by half the number of plants with corky-root symptoms. The results were used to define appropriate strategies for the sustainable management of coffee corky-root disease resistance.