Giant clams are photosymbiotic mollusks, hosting Symbiodiniaceae dinoflagellates. Serving as an alternative model organism for ecophysiological studies within reef environments, giant clams differ from corals due to their anatomical complexity, with extracellular symbionts present in multiple organs. We aimed to determine if clams, under thermal stress, exhibit symbiont shuffling both at the organism level and across individual organs. Therefore, we exposed the fluted giant clam, Tridacna squamosa, to control and heat-stress temperatures of 26 and 30 ºC, respectively, for 45 days. Subsequently, we assessed the degree of bleaching through quantification of symbiont cells and chlorophyll-a loss via fluorometric detection and photometric analysis. The relative composition of Symbiodiniaceae ITS2 rDNA profiles across ten different organs was determined using metabarcoding by next-generation sequencing. Findings show that the outer mantle of heat-stressed clams lost approximately 30% of its symbionts and 45% of the chlorophyll-a content. Extensive shuffling took place at the organism level, with the downregulation of thermally-sensitive Durusdinium phylotype D4/D5, and upregulation of thermally-tolerant, homologous and generalist phylotypes belonging to Symbiodinium and Cladocopium genera. At the organ level, shuffling took place only in the outer mantle, the only organ directly exposed to light. The other organs did not undergo compositional changes in symbiont phylotypes and may potentially serve as symbiont reservoirs. Our results illuminate the complexities of symbiont shuffling within an anatomically intricate organism, offering perspectives for other photosymbiotic reef organisms. Additionally, our study advances the knowledge regarding bleaching in giant clams, a relevant resource that has experienced substantial population declines.