Remediation of heavy metal-contaminated soils is critical due to their persistent toxicity and threat to food security and ecosystem health. Therefore, a study was conducted during September to November 2024 to assess the phytoextraction potential of Madagascar Periwinkle (Catharanthus roseus) for cadmium (Cd) and lead (Pb) in soils spiked with varying concentrations of battery scrap waste (BSW: 0, 1, 2, 3, and 4% w/w). A hybrid mechanistic-kinetic (HMK) model was developed by the integration of the Freundlich isotherm and Michaelis-Menten equations to predict bioavailable heavy metal concentrations and uptake by plants. The results showed that C. roseus had higher Cd and Pb accumulation in roots compared to shoots, with maximum concentrations of 21.504 mg/kg Cd and 43.123 mg/kg Pb observed at 4% BSW. However, increasing contamination levels significantly reduced metal removal efficiency (%), as evidenced by bioconcentration factor (BCF) and translocation factor (TF) values. Also, increasing the BSW dose significantly (p < 0.05) reduced C. roseus growth, reducing plant height, root length, biomass, chlorophyll, and carotenoid content due to heavy metal toxicity. On the other hand, Freundlich coefficients (K) and exponent (n) were useful in predicting bioavailable heavy metals. The Michaelis-Menten-based HMK model analysis showed higher maximum uptake rates (V) for Pb in roots and shoots compared to Cd, while half-saturation constant (K) values were lower in shoots compared to roots. The developed models had high R and low mean absolute error (MAE), indicating goodness of fit. This study showed that C. roseus can be used for Cd and Pb phytoextraction from contaminated soils, thereby contributing to the restoration of agro-ecosystems.