The Peruvian Upwelling ecosystem is highly productive. El Niño variability affects species abundance and distribution, and thus marine activities. Climate change is modifying El Niño patterns, compromising the strategies of marine organisms and human activities to cope with its variability. We focus on three marine social-ecological systems to identify weaknesses and leverage points for adaptation and resilience. We find that (1) the Peruvian artisanal fishery and aquaculture sectors urgently need an institutional framework for adaptation to future environmental changes; (2) bottom-up adaptation strategies require institutional support, tailored to socio-ecological specificities; and (3) additional research on socio-ecological tipping points and their effects for human-nature interactions and societal repercussions is necessary. These finding may be useful in other systems undergoing similar challenges.