Soil contamination with heavy metals is an emerging concern in the modern era, affecting all forms of life. Pigeon pea is a multi-use shrub with medicinal and nutritional values. On the basis of a randomized complete design, we investigated in the current project the combined cadmium (Cd) and copper (Cu) effect on plant growth and physio-chemical/medicinal properties of pigeon pea. Three-week-old seedlings were grown in combined Cd and Cu amended soil with increasing metal concentrations (control, 20 + 30 mg/kg, 40 + 60 mg/kg, and 60 + 90 mg/kg) for three months. At high-dose metal cumulative stress (60 + 90 mg/kg), plant shoot and root growth in terms of plant height as well as fresh and dry weight were significantly inhibited in association with decreased photosynthetic attributes (chlorophyll a and b contents, net photosynthesis, transpiration rate, stomatal conductance, intercellular CO2 concentrations) and diminished nutrient contents. Cd and Cu at high amounts inflicted oxidative stresses as assessed in elevated lipid peroxidation (MDA), hydrogen peroxide (H2O2), and electrolyte leakage contents. Antioxidant enzyme activities, namely, those of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and glutathione peroxidase (GPX), were enhanced, along with proline content with increasing metal quantity. Phenolics and flavonoids exhibited a diverse response regarding metal concentration, and their biosynthesis was significantly suppressed at high Cd and Cu cumulative stress. The reduction in secondary metabolites may account for declined medicinal properties of pigeon pea as appraised in reduced antibacterial, 2, 2-diphenyl-1-picrylhydrazyl (DPPH), and ferric-reducing antioxidant potential (FRAP) activities. Our results clearly demonstrate that the exposure of pigeon pea to Cd- and Cu-contaminated soil might affect consumers due to the presence of metals and the negligible efficacy of the herbal products.