This study investigates secondary mineralsSecondary minerals formationFormation during copperCopper sulphide leachingLeaching and their impact on pore geometry and copperCopper mobilisation. Flow-through experiments and micro-CTMicro-CT analysisAnalysis were employed to elucidate the role of secondary mineralSecondary minerals formationFormation, particularly jarositeJarosite, in influencing copperCopper dissolutionDissolution by clogging pore spaces and limiting access to the reactive surface of the copperCopper sulphide. The results indicate a high surface areaSurface area of a dissolving copperCopper sulphide mineral promotes rapid dissolutionDissolution, thereby reducingReducing the availability of Fe3+ for jarositeJarosite precipitationPrecipitation. LeachingLeaching fine particles with NaCl at low flow rateFlow rate enhanced copper recoveryCopper recovery by decreasing tortuosity and prolonging solution-ore contact, though excessive fines may cause compaction without precise flow control. Acid-only leachingLeaching promoted macroporosity evolution but reduced copperCopper yield due to proton depletion, making it suitable for ores with longer residence times or pre-treatment. Conversely, leachingLeaching under high flow ratesFlow rate in AlCl3-rich lixiviant resulted in significantly fast copperCopper dissolutionDissolution from coarse particlesCoarse particle (48.5 µmol/hr at high flow rateFlow rate vs. 9.7 µmol/hr at low flow rateFlow rate translating to over 90% copper recoveryCopper recovery at high flow rate against ~25% recoveryRecovery at low flow rate within 5 days), despite higher tortuosity and jarositeJarosite formationFormation. Moderately high Eh and acidity conditions in AlCl3AlCl3-media promotes the formationFormation of an Al-SO4 phase, further limiting Fe3⁺ availability for jarositeJarosite formationFormation. The formationFormation of precipitates during copperCopper heap leachingHeap leaching emphasises the need for robust drainage and solution management to mitigate channelling or flooding.