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Advanced technological inputs may enable profitable crop production but the agro-ecological potential of a locality can only be maximized by a reorganization of ecological principles for special production. Selection of most suitable types, addition of water supply, and provision for adequate soil fertility are most easily optimized and utilized for improvement of plants’ potential. In the work presented here, there is variation in potassium, sodium, calcium, phosphorus, iron, and zinc contents in the different compartments of Corchorus depressus under the heterogeneous environmental conditions of Indian Thar desert. The principal component analysis (PCA) was performed to synthesize the relationship and future lines of study with the help of plant biomass and community dynamics (bottom-up factor), soil parameters (top-down factors) and plant metabolites. The potassium, calcium, and iron were positively related with each other, but these elements inhibited the concentration of steroidal sapogenin and phenol at significant levels. Changes in soil nitrogen and soil phosphorus, however, favor these metabolites directly and alkaloid contents indirectly.