Summary• Here, we investigated effects of copper (Cu) and chromium (Cr) toxicity on two contrasting strains of Euglena gracilis, with and without chloroplasts, grown in culture media promoting either phototrophic or heterotrophic growth. This led to insights into Cr/Cu toxicity mechanisms and into the regulation of phototrophic vs heterotrophic metabolism.• Our data strongly suggest that in Cu 2+ and Cr 6+ stressed Euglena photosynthesis is the primary target of damage. In the applied light conditions, this was mainly damage to the photosystem II reaction centre, as shown by single-cell measurements of photochemical fluorescence quenching. Respiration and photosynthetic dark reactions were less sensitive.• The malfunctioning photosynthesis enhanced production of reactive oxygen species (mainly superoxide), leading to elevated amounts of carotenoid degradation products. At higher metal concentrations in chloroplast-containing cells, but not white cells, this oxidative stress resulted in increased respiratory oxygen uptake, likely by damage to mitochondria.• During growth in nutrient solution promoting heterotrophic metabolism, the cells were able to repair the metal-induced damage to photosynthesis, moderating the inhibition of photochemistry. Growth in medium forcing the cells into photosynthesis increased the investment in photosynthetic pigments. Comparison of the two Euglena strains surprisingly showed that the previously metal-resistant strain lost this resistance during culture.Abbreviations: Chl, chlorophyll; FKM, fluorescence kinetic microscope; F 0 , minimal fluorescence yield of a dark-adapted sample, fluorescence in nonactinic measuring light; F m , maximum fluorescence yield of a dark-adapted sample; F v /F m = (F m -F 0 )/ F m , maximal photochemical quantum yield of PSII in dark-adapted state; [hms]-Chl, heavy metal substituted Chl (i.e. Chl in which the central ion, Mg 2+ , is replaced by a heavy metal ion); Mg-substitution, substitution of the natural central ion of Chl, Mg 2+ , by heavy metals; NPQ, nonphotochemical quenching -in this paper, we measure nonphotochemical quenching as q CN = (F m − F m ′)/F m , 'complete non-photochemical quenching of Chl fluorescence', i.e. with normalisation to F m ; PSII, photosystem II; RC, photosynthetic reaction centre; Sm, Streptomycin; Φ PSII = Φ e = (F m ′ − F t ′)/F m ′, effective quantum yield of photochemical energy conversion in actinic light. Values of this parameter were also calculated for the relaxation period after the end of actinic light in order to follow the return of the system to its dark-acclimated state as measured by F v /F m .