Under homoeostatic conditions, the relationship between the coralPocillopora damicornisandVibrio coralliilyticusiscommensal. An increase in temperature, or in the abundance ofV. coralliilyticus, can turn this association pathogenic,causing tissue lysis, expulsion of the corals’symbiotic algae (genusSymbiodinium), and eventually coral death. Using acombination of microfluidics,fluorescence microscopy, stable isotopes, electron microscopy and NanoSIMS isotopicimaging, we provide insights into the onset and progression ofV.coralliilyticusinfection in the daytime and at night, atthe tissue and (sub-)cellular level. The objective of our study was to connect the macro-scale behavioural response ofthe coral to the micro-scale nutritional interactions that occur between the host and its symbiont. In the daytime, polypsenhanced their mucus production, and actively spewed pathogens.Vibrioinfection primarily resulted in the formationof tissue lesions in the coenosarc. NanoSIMS analysis revealed infection reduced13C-assimilation inSymbiodinium, butincreased13C-assimilation in the host. In the night incubations, no mucus spewing was observed, and a mucusfilm wasformed on the coral surface.Vibrioinoculation and infection at night showed reduced13C-turnover inSymbiodinium, but didnot impact host13C-turnover. Our results show that both the nutritional interactions that occur between the two symbioticpartners and the behavioural response of the host organism play key roles in determining the progression and severity ofhost-pathogen interactions. More generally, our approach provides a new means of studying interactions (ranging frombehavioural to metabolic scales) between partners involved in complex holobiont systems, under both homoeostatic andpathogenic conditions.