Abstract To explore the mechanism(s) of survival of the organism in acid- and metal-stressed environment and to test certain hypotheses, the growth rates, uptake of NH + 4, Na +, K +, Ca 2+, NO − 3, PO 3− 4, efflux of Na + and K +, activities of nitrate reductase, acid phosphatase and ATPase and internal pH of an acid-tolerant and an acid-sensitive strain of Chlorella vulgaris exposed to Cu and Ni at different pHs (pH 6.8, 5.0, 4.0 and 3.5) were compared. A general reduction in all variables was noticed with decrease in pH; however, the acid-tolerant strain was metabolically more active than the acid-sensitive strain. Reduced cation (NH + 4, Na +, K +, Ca 2+, Cu 2+ and Ni 2+) uptake coupled with an increased concentration of anions (NO − 3 and PO 3− 4) supported the hypothesis of the development of positive membrane/zeta potentials in the acid-tolerant strain. Further an accelerated accumulation of NO − 3 and PO 3− 4 in the cells and a significant increase in ATPase activity with decreasing pH also supported our postulates that these processes are responsible for regulating the internal pH at neutrality in the acid-tolerant strain either by exporting H + ions into the external medium or by producing OH − ions from NO − 3. The lower toxicity of Cu and Ni to the acid-tolerant strain compared to the acid-sensitive strain also supported our hypothesis of low metal uptake in the acid-tolerant strain due to cation repulsion by the membrane having low permeability and positive zeta and membrane potentials. The development of a superactive ATPase and a change in membrane potential and permeability not only offer protection against acidity by keeping internal pH neutral but also confer co-tolerance to metals.