Metals in traces are vital for microalgae but their occurrence at high concentrations in habitats is a serious ecological concern. We investigated the potential of two acid-tolerant microalgae, Desmodesmus sp. MAS1 and Heterochlorella sp. MAS3, isolated from neutral environments, for simultaneous removal of heavy metals such as copper (Cu), iron (Fe), manganese (Mn) and zinc (Zn), and production of biodiesel when grown at pH 3.5. Excepting Cu, the selected metals at concentrations of 10-20 mg L-1 supported good growth of both the strains. Cellular analysis for metal removal revealed the predominance of intracellular mechanism in both the strains resulting in 40-80 and 40-60% removal of Fe and Mn, respectively. In-situ transesterification of biomass indicated enhanced biodiesel yield with increasing concentrations of metals suggesting that both these acid-tolerant microalgae may be the suitable candidates for simultaneous remediation, and sustainable biomass and biodiesel production in environments like metal-rich acid mine drainages.