Coffee (Coffea spp.) is one of the world's most valuable agricultural export commodities produced by small‐scale farmers. Its germplasm, which holds useful traits for crop improvement, has traditionally been conserved in field genebanks, which presents many challenges for conservation. New techniques of in vitro and cryopreservation have been developed to improve the long‐term conservation of coffee. But a question remains as to whether these new techniques are more cost effective than field collections and more efficient at reducing genetic erosion. This study compared the costs of maintaining one of the world's largest coffee field collections with those of establishing a coffee cryo‐collection at the Centro Agronómico Tropical de Investigación y Enseñanza (CATIE) in Costa Rica. The results indicate that cryopreservation costs less (in perpetuity per accession) than conservation in field genebanks. A comparative analysis of the costs of both methods showed that the more accessions there are in cryopreservation storage, the lower the per‐accession cost. In addition to cost, the study examined the advantages of cryopreservation over field collection and showed that for species that are difficult to conserve using seeds, and that can only be conserved as live plants, cryopreservation may be the method of choice for long‐term conservation of genetic diversity.