Microbial processes sour oil, corrode equipment, and degrade hydrocarbons at an annual global cost to the oil and gas industry of nearly $2 billion. However, top-down control of these microbial processes can reduce their damage and enhance oil recovery. Here, we screened microbial communities from five oil wells in the Illinois basin and evaluated nutrient injection strategies to control metabolism and community composition. Molasses and molybdate supplementation stimulated significant gas and organic acid production while completely suppressing corrosive H2S formation in samples from two wells. These changes were accompanied with significant shaping of the microbiome community. Simulations of field operations via a lab-scale mini-coreflood validated that oil well microbiomes can be engineered to also shape oil hydrocarbon composition in situ. These pilot studies validate the potential of economical and sustainable top-down microbiome engineering to control microbes in oil extraction and enhance the economic viability of oil recovery.