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Soil in mining areas is typically highly contaminated with heavy metals and lack essential nutrients for plants. Phosphorus reduces oxidative stress, improves plant growth, composition, and cellular structure, as well as facilitates the phytoremediation potential of fibrous crop plant species. In this study, we investigated two jute (Corchorus capsularis) varieties HongTieGuXuan and GuBaChangJia cultivated in copper (Cu)-contaminated soil (2221 mg kg−1), under different applications of phosphorus (0, 30, 60, and 120 kg ha−1) at both anatomical and physiological levels. At the same Cu concentration, the tolerance index of HongTieGuXuan was higher than that of GuBaChangJia, indicating that HongTieGuXuan may be more tolerant to Cu stress. Although the normal concentration of P (60 kg ha−1) in the soil improved plant growth, biomass, chlorophyll content, fibre yield and quality, and gaseous exchange attributes. However, high concentration of P (120 kg ha−1) was toxic to both jute varieties affected morphological and physiological attributes of the plants under same level of Cu. Moreover, Cu toxicity increased the oxidative stress in the leaves of both jute varieties was overcome by the activities of antioxidant enzymes. Furthermore, the high concentration of Cu altered the ultrastructure of chloroplasts, plastoglobuli, mitochondria, and many other cellular organelles in both jute varieties. Thus, phytoextraction of Cu by both jute varieties increased with the increase in P application in the Cu-contaminated soil. This suggests that P application enhanced the phytoremediation potential jute plants and can be cultivated as fibrous crop in Cu-contaminated sites. Image 1 • External application of P is pre-requisite for the better growth in jute under stress condition. • The variety HongTieGuXuan was proved more tolerant as compared to GuBaChangJia. • Application of P assisted phytoextraction of Cu in both jute varieties. • Phytotoxicity of Cu destroy ultra-structure of chloroplast. • Plant has strong antioxidant defence system to tolerate Cu-stress. [ABSTRACT FROM AUTHOR]