The ‘post-antibiotic’ era is near according to the World Health Organization (WHO). It is well known, due to the work of the scientific community, that drugs (antibiotics, antifungals, and other antimicrobial agents) are continuously becoming less effective, and multidrug-resistant (MDR) pathogens are on the rise. This scenario raises concerns of an impending global infectious disease crisis, wherein a simple opportunistic infection could be deadly for humans. The war against MDR pathogens requires innovation and a multidisciplinary approach. The present study provides comprehensive coverage of relevant topics concerning new antimicrobial drugs; it suggests that a combination of different natural products (such as plant extracts, honey, propolis, prebiotics, probiotics, synbiotics, and postbiotics), together with drug therapy, could be used as an adjuvant in standard treatments, thus allowing drug sensitivity in MDR pathogens to be restored, host immunity to be enhanced, and clinical efficiency to be improved. Currently, new and relevant developments in genomics, transcriptomics, and proteomics are available for research, which could lead to the discovery of new antimicrobial drugs and a new generation of antibiotics and non-antibiotics. However, several areas concerning natural products and their combination with standard drugs remain unclear. In an effort to advance new therapies for humankind, these gaps in the literature need to be addressed.