Marine food webs are being reshaped by rapid environmental change, yet empirical evidence of community-wide trophic change over multiple decades remains scarce. As part of the Southern and Eastern Australian Marine Ecosystems (SEA-MES) project, we used stable carbon and nitrogen isotopes to compare trophic structure across particulate matter and 34 consumer taxa in south-east Australia between the 1990s and 2020s. Contemporary sampling spanned four SEA-MES research voyages across northern and southern regions of this rapidly warming ecosystem. Over three decades, baseline δ¹⁵N declined substantially, yet most consumers showed significant δ¹⁵N enrichment, corresponding to widespread increases in estimated trophic position. Changes in δ¹³C and isotopic niche width varied among taxa, indicating restructuring of carbon pathways and trophic niches rather than a uniform ecosystem response. At the community level, isotopic niche overlap increased markedly in northern and southern waters relative to the 1990s. Together, these changes reveal substantial reorganisation of trophic pathways over three decades, characterised by increasing trophic convergence and reduced functional separation among consumers in one of the world’s most rapidly warming marine ecosystems.