Electrokinetic in situ leaching (EK-ISL) of copper sulphides is a novel mining technology aimed at recovering copper from orebodies without physical excavation, thereby significantly reducing the environmental footprint of the mining operation. Its viability at larger scale is, however, highly dependent on developing a comprehensive understanding of the geochemical processes occurring inside the pore space of the intact rocks during leaching. One of the critical issues affecting the efficiency of copper sulphide leaching operations is the formation of secondary layers. So far, the details of their formation have only been studied under ex situ conditions and for ground samples. Therefore, this study was aimed at a detailed characterisation of the secondary leaching products under EK-ISL induced leaching conditions and how they evolved over time. We conducted time-dependant leaching tests on intact core samples with either ferric chloride or ferric sulphate as lixiviant. SEM-EDS and laser Raman microspectroscopy showed the formation of elemental sulphur as a result of the oxidation of longer-chain polysulphides. The neo-formed phases showed to slow down copper recovery, yet did not completely halt the leaching progress. Our conceptual model of the secondary layer formation suggests that the sustained dissolution of polysulphides during EK-ISL-induced leaching under the induced geochemical conditions exposes new mineral surfaces to attack. Importantly, this creates the opportunity for secondary phase re-solubilisation and therefore enhanced copper recovery.