Provided are methods for diagnosing, monitoring and mitigating microbiologically influenced corrosion (MIC). The methods employ steps to determine the nature and concentration of biological signatures, formed through metabolism of microorganisms, and correlating the biological signatures with MIC. Based on such analyses, appropriate MIC mitigation strategies may be implemented so as to efficiently target MIC at sites of interest. The methods advantageously allow selection of appropriate MIC mitigation treatments that correspond to the level of severity of the MIC and based on historical data correlating particular biological signatures with particular MIC risk.