Antibiotic resistance is a pressing global health issue, leading to increased illnesses and fatalities. The contribution of viruses to the acquisition, preservation, and dissemination of antibiotic resistance genes (ARGs) is not yet fully understood. By using a high-throughput functional gene-based microarray (GeoChip 5.0), this study examines the prevalence and relative abundance of bacteriophage and eukaryotic viral genes in swine manure, compost, compost-amended agricultural soil, and unamended soil from suburban regions of Beijing, China. Our findings reveal a significantly elevated presence of biomarker viral genes in compost-amended soils compared to unamended soils, suggesting potential health risks associated with compost fertilization. We also observed stronger ecological interactions between ARGs and viral genes in manure and compost than in soils. Network analysis identified arabinose efflux permeases and EmrB/QacA resistance genes, linked to CRISPR encoding sequences, as keystone nodes, indicating possible ARG acquisition via virus infections. Moreover, positive correlations were found between viral genes, antibiotic concentrations, and ARG diversity in manure, compost, and compost-amended soils, highlighting a likely pathway for virus-mediated ARG transfer. In summary, our results indicate that use of compost as a fertilizer in agricultural settings could facilitate the spread of ARGs through viral mechanisms, allowing for time-delayed genetic exchanges over broader temporal and spatial scales than ARGs within bacterial genomes.