Formation damage issues typically arise at different recovery stages of unconventional oil/gas and geothermal energy in various petroleum and hydrological geosystems. A lack of understanding of the potentially induced damage in those geosystems is associated with downside risks and negative economic consequences. As a comprehensive review and analysis building upon our previous work (Yuan and Wood, 2018), this paper aims to raise more awareness of the mechanically, chemically, biologically and thermally induced damage issues associated with oil/gas and geothermal energy recovery in unconventional shale, coal-bed methane, geothermal reservoirs, and deepwater oilfields. It does so by integrating state-of-the-art modelling, laboratory experiments and field examples. Potential formation damage issues are discussed in the context of each specific geosystems to answer why, where and when damage occurs, its extent and impacts, and how to control, prevent and take advantages of such issues. Moreover, an integrated risk and opportunity assessment and management framework is presented with the objective of improving the outcomes of energy extraction projects in practice.