This study concerns the metabolism of polyphosphate in Trichoderma harzianum, a biocontrol agent with innate resistance against most chemicals used in agriculture, including metals, when grown in the presence of different concentrations of cadmium. The biomass production was affected by the concentration of metal used. Control cultures were able to accumulate polyphosphate under the conditions used. Moreover, the presence of cadmium induced a reduction in polyphosphate content related to the concentration used. The morphological/ultrastructural aspects were characterized by using optical and scanning electron microscopy, and were affected by the heavy metal presence and concentration. The efficiency of cadmium removal revealed the potential of the microorganism for use in remediation. The data indicate the potential for polyphosphate accumulation by the fungus, as well as its degradation related to tolerance/survival in the presence of cadmium ions.