Hybrid drugs are multi-target chimeric chemicals combining two or more drugs or pharmacophores covalently linked in a single molecule. In the field of anti-infective agents, they have been proposed as a possible solution to drug resistance issues, presumably having a broader spectrum of activity and less probability of eliciting high level resistance linked to single gene product. Although less frequently explored, they could also be useful in the treatment of frequently occurring co-infections. Here, we overview recent advances in the field of hybrid antimicrobials. Furthermore, we discuss some cutting-edge approaches to face the development of designed multi-target agents in the era of omics and big data, namely analysis of gene signatures and multitask QSAR models.