The spread of antibiotic resistance in bacteria is a matter of global concern, and the identification of possible sources of the associated genetic elements (antibiotic resistance genes -ARGs-, components of the horizontal gene transfer mechanism), is becoming an urgent need. While the transmission of ARGs in medical settings have been adequately characterized, ARG propagation in agroecosystems remains insufficiently studied. Particularly crucial is the determination of potential risks associated to the use of swine slurries and related products as component of organic fertilizers, an increasingly used farming practice. We determined ARGs and antibiotic loads analysed from swine slurries and digestates from eight farms from Catalonia (NE Spain), and compared the results with their microbiome composition. Both ARGs and antibiotic were conspicuous in farm organic wastes, and the levels of some antibiotics exceeded currently accepted minimum inhibitory concentrations. Particularly, the presence of high loads of fluoroquinolones was directly correlated to the prevalence of the related qnrS1 ARG in the slurry. We also found evidence that ARG loads were directly correlated to the prevalence of determined bacterial taxa (Actinobacteria, Proteobacteria, Spirochaeta), a parameter that could be potentially modulated by the processing of the raw slurry prior to their use as fertilizer.