Antibiotic contamination from biogenic waste in agricultural soils poses a significant threat to soil health and crop productivity. We investigated the effect of antibiotics on the soil microbial community, antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) and plant productivity in a six-week greenhouse trial. Here, Spinacia oleracea (spinach) and Raphanus sativus (radish) were grown from seed and a mix of five antibiotics, namely sulfamethoxazole, trimethoprim, enrofloxacin, clarithromycin and chlortetracycline, were added to the soil at concentrations 0, 0.1, 1 and 10 mg kg-1 soil dry weight (c0, c0.1, c1 and c10, respectively). Overall, we found that the antibiotic treatments significantly impacted prokaryotic α-diversity and prokaryotic and fungal β-diversity. Human and plant pathogen relative abundance did not increase under antibiotic exposure, but there was a significant reduction of plant growth-promoting bacteria. Moreover, the c10 treatment significantly increased the abundance of MGE intI1 indicative of horizontal gene transfer and sulfonamide resistance gene sul1 and significantly lowered radish biomass and nitrogen uptake, while spinach biomass and nitrogen uptake were unaffected. In summary, our study showed that antibiotic exposure significantly changed prokaryotic community diversity, while fungi remained largely unaffected. The reduction of plant growth-promoting bacteria may have a significant impact on soil nutrient cycling and crop productivity, but more research is needed to understand the long-term impact of these co-applied antibiotics on food production. Additionally, more studies are needed to understand the effect of antibiotics on realistic, field scale, conditions to fully understand the impact on environmental and human health.