Abstract: Rising copper (Cu) demand and a growing inventory of Cu-bearing mine wastes highlight their potential as alternative resources; however, re-extraction remains challenging. Electrokinetic in situ leaching (EK-ISL) offers a non-invasive alternative but its biofunctional consequence on post-treated material remains unknown. Here, we examine the potential impact of citric acid-aided (0.5 M) EK-ISL on community-wide microbiome response under laboratory conditions through 16S rRNA metabarcoding. Citric-driven electrokinetically-induced conditions resulted in efficient Cu leaching but altered soil bacterial ecology, leading to the expansion of copiotrophic (Proteobacteria) over oligotrophic (Chloroflexi) taxa. Functional predictions based on taxonomic information suggested a shift supporting traits linked to rapid growth and niche colonization. Despite microbiome restructuring, our findings argue in favor of citric acid as a soil amendment, rather than a harmful contaminant by allowing key pedogenic functions like nitrogen fixation to persist. These findings highlight citric acid’s potential to balance efficient metal extraction with ecological recovery.