In recent years there has been a growing interest in the use of natural antimicrobial compounds to limit or avoid the use of chemical antimicrobials. Natural antimicrobial compounds can come from plants (essential oils) or from microorganisms (bacteriocins, mycocines, and active peptides). Despite a wide range of possible applications, their exploitation at the industrial level is still limited and needs to be investigated. The actual and possible applications of natural antimicrobial compounds in agri-food are a growing research field. In addition to the use of antimicrobial compounds, microorganisms themselves can be used in the control of spoilage microorganisms along the entire production chain of the agri-food industry. Likewise, the papers collected in this Special Issue indicate the fast development of novelties in this research field.