<p>Sea cucumbers are highly valued commercial species in the seafood industry. However, their hatchery and commercialization are constrained by the high mortalities experienced by these animals driven by environmental changes and physiological stress. Under such conditions, functional alterations in their immune system can induce integument ulcers that are later infected by opportunistic pathogens. Sea cucumbers, however, can display defense mechanisms that enable self-healing and recovery. It has been hypothesized that such mechanisms are assisted by changes in the skin-associated microbial community, enhancing the resilience of infected animal hosts. Here, we investigated the dynamics of the skin-associated microbiomes during infection and recovery of the tropical sea cucumber <i>Holothuria scabra</i>. Our findings reveal that the acclimation process for both, the host and the microbiome occurs simultaneously, with the latter gradually resembling the surrounding water environment after one month. The gradual healing of the sea cucumber skin and the structural changes in the associated microbiome were concurrent to the decline of pathogenic bacteria and the increase in the abundance of the family <i>Rhodobacteraceae</i>. The enrichment of some members from this group (genus <i>Ruegeria</i>) suggests a potential beneficial role in facilitating sea cucumber host recovery and acclimation. Our study provides valuable insights into the dynamics of the skin microbiome in sea cucumbers, highlighting the key role of this organismal trait for the resilience and overall health of the sea cucumber host.</p>