Copper (Cu) is an abundant essential micronutrient element in various rocks and minerals and is required for a variety of metabolic processes in both prokaryotes and eukaryotes. However, excess Cu can disturb normal development by adversely affecting biochemical reactions and physiological processes in plants. However, organic soil is rich in micronutrients and can assist plants to tolerate toxicity by promoting growth and biomass. This study explored the potential of organic and Cu-contaminated soil on fibrous jute (Corchorus capsularis ). Plants were grown in the organic soil, natural soil (normal soil) and Cu-contaminated soil for 60days, and we studied different growth, physiological and ultra-structure alterations in the plant. Results showed that the addition of organic acid in the soil showed a remarkable increase in seed germination, plant height, fresh biomass, photosynthetic pigment and gas exchange parameters, and decreased the malondialdehyde (MDA) concentration in the tissues when compared to the plants grown in the natural soil. In contrast, plants grown in the Cu-contaminated soil significantly (P <0.05) decreased the seed germination, plant height, fresh biomass, photosynthetic pigment and gas exchange parameters, and increased MDA content, proline concentration and the activities of various antioxidant compounds; i.e. peroxidase (POD) and superoxidase dismutase (SOD). In addition, Cu toxicity also destroyed many membrane bounded organelles especially the chloroplast, which was revealed from transmission electron microscopy (TEM). We concluded that Cu toxicity affected growth and physiological attributes in C. capsularis , while addition of organic soil increased plant growth and biomass.