Copper pollution can alter biological and trophic functions. Organisms can set up different tolerance strategies, including accumulation mechanisms (intracellular vacuoles, external chelation, etc.) to maintain themselves in copper-polluted environments. Accumulation mechanisms can influence the expression of other phenotypic traits, allowing organisms to improve their fitness. Whether copper effects on accumulation strategies interact with other environmental stressors such as temperature and how this may differ within species are still unsolved questions. Here, we tested experimentally whether the combined effect of copper and temperature modulates traits linked to fitness, morphology, movement and accumulation in six strains of the ciliate Tetrahymena thermophila. We also explored whether copper accumulation might modulate environmental copper concentration effects on phenotypic and fitness traits. Results showed high intraspecific variability in the phenotypic and fitness response to copper, with interactive effects between temperature and copper. In addition, they suggested an attenuation effect of copper accumulation on the sensitivity of traits to copper, but with great variation between strains, temperature and copper concentration. Diversity of responses among strains and their thermal dependencies pleads for the integration of intraspecific variability and multiple stressors approaches in ecotoxicological studies, thus improving the reliability of assessments of the effects of pollutants on biodiversity.