Microalgae are able to adapt and to synthesize valuable compounds in response to abiotic stresses such as temperature, UV-radiation or metallic trace elements. We studied this faculty of adaptation by assessing the impact of high metal concentrations on Heterocapsa cf. bohaiensis, a newly isolated dinoflagellate from the New Caledonian coastal water rich in metals. We cultivated H. cf. bohaiensis in continuous culture mode using 10L photobioreactors and exposed the algae to high concentrations (10-3M) of nickel (Ni2+) and/or iron (Fe2+). We then followed its photosynthetic efficiency using Pulse Amplitude Modulated chlorophyll fluorometry and its metabolome with targeted (HPLC-UV-DAD, GC-MS) and non-targeted (LC-MS2 and NMR) approaches. The photosynthetic measurements indicate that H. cf. bohaiensis is tolerant to Ni2+ but sensitive to Fe2+ high concentrations. In presence of Fe2+, Fv/Fm and rETRm decreased from 0.62 to 0.47 and from 156 to 102, respectively. The JIP-tests (i.e. the fast chlorophyll fluorescence transient) suggest that the reduction of photosynthesis in response to Fe2+ is due to a disruption in the electron transport chain rather than a defect in the PSII light absorption and trapping which are on the contrary enhanced by Fe2+. The metabolomics analyses highlight the variation of the main dinoflagellate pigments, Chlorophyll c and a, peridinin, diadinoxanthin and diatoxanthin in response to time and metals and give a first glimpse on the complex metabolomic response to metal stress. These results bring new knowledge on this species and on the impact of nickel and iron on the microalgae photosynthetic pathway and metabolomic responses.