Anopheles arabiensis is a major malaria vector in Southern Africa. This vector displays plastic behaviour in terms of feeding and resting behaviour. It is also one of the members of the An. gambiae complex adapting to breeding in polluted waters. Heavy metal pollution is a common effect of anthropogenic activities. This is prevalent in both rural and urban areas. While heavy metals are toxic in high concentrations, some serve as critical micronutrients. These include iron, copper, nickel, zinc and cobalt. Zinc is essential for enzyme activity and cobalt is involved in vitamin synthesis. These metals contribute to insect development, reproduction, and immunity, often interacting with the insect’s microbiota in a complex manner. There can be a variety of concentrations of these pollutants in both urban and rural bodies. This study aimed to determine whether zinc and cobalt could have positive effects at lower concentration on the major malaria vector Anopheles arabiensis. Sublethal concentrations were assessed for zinc and cobalt for the insecticide susceptible An. arabiensis strain SENN and the insecticide resistant strain SENN-DDT. Although these strains did not differ significantly in their tolerance at first instar, these low doses did become cumulatively toxic. Low doses of zinc and cobalt had differential effects on the two strains. Zinc had a positive effect on the development of SENN, while cobalt has a positive effect on the larval development of SENN-DDT. Similarly, these low doses increased longevity in both strains. These larval exposures also had variable effects on the oxidative stress response and gut microbial composition and diversity of both strains. KEGG analysis also indicated a variability between strains in response to the metal exposure. These findings highlight that heavy metal exposure is not necessarily negative, but dependent on concentration. This has implications for the potential expansion of An. arabiensis into urban areas.