This paper examines various fishery management scenarios based on the recovery of small-scale fisheries (SSF) following a submarine volcanic eruption in 2011 in El Hierro Island (Canary Islands, Spain). After this catastrophic event, the SSF composition of La Restinga fishing community was affected by socio-economic and demographic changes. The uncertainty derived from this situation provides an opportunity to evaluate the fisheries’ sustainability and advice on different management options under an ecosystem-based approach. The Ecopath with Ecosim modeling framework was used to build a model of El Hierro Island, where the versatile and traditional multispecies small-scale fleet of La Restinga operates. Our main goal is to improve traditional fisheries, based on the relevance of key local fisheries and multi-specific fishery strategies in the light of scientific knowledge. Temporal simulations for the next decade were analyzed by creating scenarios of alternative fishing effort distributions based on the fishing trends observed in El Hierro small-scale community of La Restinga after a natural hazard. The outcomes of this modeling prototype show the vulnerability of some littoral and demersal species, the resilience of migratory species, and the sustainability of SSF diversification practices. These results could develop an adaptive and co-management strategy with the local fishing community to preserve the small-scale fishing system and marine resources.