Eco-friendly antimicrobial alkali-activated slag (AAS) binders show great promise in newly designed and existing wastewater infrastructure threatened by microbial induced concrete corrosion (MICC). This work investigates the antimicrobial performance and biodegradation mechanisms of a new benzoate (BZ)-modified AAS binder. The bacterial activity, corrosion morphology, and material degradation mechanisms, of the novel BZ-modified antimicrobial AAS post-simulated MICC tests are analysed. The bacterial activity assessments (pH value, sulphate concentration, and live/dead staining) results demonstrate the remarkable antimicrobial efficacy of BZ-modified AAS in killing sulphur-oxidising bacteria A. thiooxidans and inhibiting biogenic acidification. The BZ-modified AAS demonstrates excellent microbial corrosion resistance with greatly suppressed production of deleterious gypsum and corrosion depth. The mechanisms of biodeterioration of antimicrobial AAS matrix are revealed, suggesting the nanoscale rupture of calcium-aluminosilicate-hydrate (C-A-S-H) in short chains and networking of aluminosilicate unites upon the removal of interlayer CaO polyhedral. The removal of Al-tetrahedra from bridging sites of C-A-S-H is more susceptible than that of Si-tetrahedra in AAS pastes under microbial corrosion. This study has demonstrated the potentials of novel antimicrobial AAS-based concrete as the next-generation construction materials for wastewater infrastructure.