The impacts of natural- and human-induced processes on lake ecosystems in remote oceanic islands remain to be fully elucidated. These lakes are excellent candidates to analyze the importance of anthropogenic vs. natural forces driving lacustrine long-term ecological evolution from previous pristine pre-colonized conditions. Disentangling the effects of both is particularly relevant in highly active volcanic areas, where catastrophic eruptions can act as an atypical natural driver altering the lake's long-term ecological trajectories. In this paper we study past ecological changes occurring in Lake Azul (São Miguel island), a crater lake from the remote Azorean archipelago, to address which were the main causes of its long-term trophic history. We analyzed diatom assemblages, sedimentology, and bulk organic matter of sediments deposited since ca. 1290 CE, when a huge local eruption occurred. This episode drove the evolution of Lake Azul through six distinct phases, commencing with a restart of ecological succession after tephra deposition disrupted biogeochemical cycling. The alteration was so profound that the lake underwent a state of oligotrophic conditions for approx. 650 yr. Nutrients were sourced by fish-induced internal recycling and the overflow of the near Lake Verde during this period, rather than by allochthonous nutrient inputs modulated by climate variability and/or vegetation cover changes in the watershed after the official Portuguese colonization. It was only after recent artificial fertilization when the system overcame the volcanic-induced long-term resilience. This over-fertilization and a reduction in water turnover exacerbated the recent symptoms of eutrophication after 1990 CE. Contrary to other studies, Lake Azul constitutes an uncommon case of long-term resilience to trophic change induced by a cataclysmic volcanic eruption. It brings new insights into the fate of lake ecosystems which might be affected by similar events in the future.