The exchange of metabolites between photosynthetic symbionts and their coral host in shallow-water scleractinians provides the nutritional basis for their successful evolution and the existence of massive coral reefs in oligotrophic tropical waters. Autotrophic nutrition, based on carbon- and nitrogen-rich photosynthetic metabolites, is complemented by heterotrophic uptake and assimilation of organic matter to obtain additional carbon, nitrogen and phosphorus. By combining TEM ultrastructural observations with quantitative NanoSIMS isotopic imaging of tissue sections at sub-cellular resolution, we have compared the exchange of nutrients from the autotrophic assimilation of 15N-nitrate and 13C-bicarbonate with the heterotrophic uptake from 15N- and 13C-labelled brine shrimps in Stylophora pistillata from the Red Sea. Our results confirm that heterotrophy serves as the dominant source of nitrogen for the coral holobiont. On a time scale of 6 hours, heterotrophy provided approximately nine times more nitrogen to the host gastrodermal anabolism than symbiont nitrate fixation and translocation. Heterotrophic nitrogen was also used in anabolic processes in the symbionts, but at a level about 40% lower compared with nitrogen incorporation from nitrate fixation. The role of photosynthesizing symbionts the major contributors of carbon to the coral host was evident from the observation that autotrophic carbon enrichment in the gastrodermal layer was seven times higher in comparison to the heterotrophic carbon acquisition. Our observations directly demonstrate the complementing roles of heterotrophic and autotrophic food acquisition and support the notion that recycling of nutrients in symbiotic coral holobionts is critical to their vitality. The effects of stress from environmental change, including increasing water temperature and ocean acidification, are under investigation.