Hydrogen sulfide (H2S) biogenesis in oil reservoirs, termed “bio-souring,” poses significant health and environmental costs. Here we assessed the use of perchlorate (ClO4-) as a bio-souring inhibitor in a simulated North Sea oil reservoir system consisting of sand-packed columns saturated with crude oil with reservoir-sourced waters as the sole inoculum source. We compared biogeochemistry to specific microbial populations using a combination of 16S rRNA gene sequencing and genome-resolved metagenomics. Sulfide biogenesis commenced only after the addition of volatile fatty acids (VFA) in concentrations similar to that of reservoir-produced fluids. However, cumulative sulfide production was 1.7-fold the expected value based on injected VFA, indicating consumption of crude oil components by the microbial community. Community analysis showed the Desulfotomaculum spp. as the dominant sulfate reducing microbes (SRM; 26-74%) in H2S-producing conditions. Initially, a weekly perchlorate pulsed dosing (16.8 mM) provided no significant (P>0.05) decrease in the sulfide production and the average perchlorate retention was less than 2 mM (IC42). However, both bi-weekly pulsed and continuous treatments inhibited H2S production completely; average perchlorate retention in the bi-weekly dosing was 2.8 mM (IC65). Inhibition of sulfate reduction was corroborated by a significant (P<0.05) and faster decline in putative sulfate-reducing bacteria. Similarly, perchlorate degradation in the column corresponded to an increased in the relative abundance of putative perchlorate-reducing bacteria. Metagenome-assembled genomes (MAGs) supported trends observed in community analysis, identifying genes for dissimilatory sulfate reduction in MAGs Desulfotomaculum FMC-1, Desulfotomaculum FMC-2, Desulfovibrionales DPB-1, Desulfotignum DPB-2, Desulfovibrio DPB-3, and Acidobacteria ACD-1 and genes for dissimilatory perchlorate reduction in MAGs Sedmenticola GPB-1, Sedmenticola GPB-2, and Rhodocylcaceae BPB-1. The growth of perchlorate-reducing bacteria supports a model of H2S inhibition through the bio-competitive exclusion of sulfate-reducing microorganisms.