This study explores the utility of Fourier transform infra-red spectroscopy (FT-IR) as a metabolomic tool to detect changes in water-extractable chemical profile resulting from horizontal gene transfer (HGT) events in artificial soil slurries. A GFP–Km (Green fluorescent protein–kanamycin) cassette tagged HGT recipient Acinetobacter strain ADPWH67 with the salicylate hydroxylase gene (salA) disrupted was introduced to slurries containing either sterile or non-sterile soil. The subsequent addition of naked salA DNA allowed the specific monitoring of HGT events by enumerating GFP-expressing colonies on minimal media with salicylate as a sole carbon source. DNA sequencing confirmed that salA was restored in these transformants. Gene transformation frequencies of around 10−6 were achieved in the presence of sterile and non-sterile soils. Aqueous extracts of the soil slurries were then analyzed using FT-IR in order to ascertain whether any shifts in chemical profile could be detected. We found that following HGT events FT-IR chemical profiles were clearly altered when analyzed with multivariate statistics. Furthermore, these changes could be explained by differences in key chemical signatures including salicylate as well as other biomolecules found in soils. The slurry extracts were also subjected to GC-MS which confirmed the results of FT-IR analyses. FT-IR was therefore demonstrated to have utility for the rapid screening of metabolomic changes in soils following effective HGT events. In addition, this approach could potentially link specific metabolite changes with corresponding catabolic genes.