Oceanic islands have been the grand stage of documented extinctions. In view of limited resources, efficient prioritization is crucial to avoid the extinction of taxa. This work lists the top 100 management priority species for the European archipelagos of the Macaronesian region (Azores, Madeira and the Canary Islands), taking into account both their protection priority and their management feasibility. Bryophytes, vascular plants, molluscs, arthropods and vertebrates were scored by species experts following two sets of criteria: (i) protection priority, including ecological value, singularity, public institutions’ management responsibilities and social value; (ii) management feasibility, including threats knowledge and control feasibility, external socio-economical support for management and biological recovery potential. Environmental managers weighted the same criteria according to their management importance. Final species scores were determined by the combination of both species valuation and criteria weighting. Vascular plants dominate the Top 100 list, followed by arthropods and vertebrates. The majority of listed taxa are endemic to one archipelago or even to a single island. The management feasibility criteria did not dictate that all taxa must be eminently endangered, as for most of the species it should be relatively easy to control threats. The main advantages of this process are the independent participation of scientists and conservation managers, the inclusion of criteria on both protection priority and management feasibility and the taxonomically unbiased nature of the process. This study provides a potentially useful biodiversity conservation tool for the Macaronesian archipelagos that could be readily implemented by the respective regional governments in future legislation.