Eutrophication coupled with ocean warming and acidification (OWA) poses pervasive threats to coastal plankton ecosystems worldwide. How these co-occurring stressors modulate ecosystem recovery following nutrient abatement remains poorly understood. Here, using a subtropical mesocosm experiment integrating community trajectory analysis, molecular co-occurrence networks and carbon-flow food-web modelling, we show that nutrient reduction partially restores plankton community structure in the absence of OWA. By contrast, OWA redirects ecosystem recovery following nutrient reduction towards alternative states characterized by diatom dominance, the proliferation of copiotrophic bacteria and plankton miniaturization. Although community composition remains persistently divergent from control baselines, rewired species interactions and restored top–down grazing help sustain biodiversity, network stability and trophic functioning. This multiscale decoupling suggests that ocean climate change can redirect eutrophic ecosystems towards structurally novel but partially functional configurations, rather than merely delaying recovery. Our findings highlight the need for climate-adaptive nutrient management and multidimensional assessments of resilience to safeguard coastal ecosystems under ongoing OWA