Bacterial infections represent one of the major causes of mortality worldwide. Therefore, over the years, several nanomaterials with antibacterial properties have been developed. In this context, clay minerals, because of their intrinsic properties, have been efficiently used as antimicrobial agents since ancient times. Halloysite nanotubes are one of the emerging nanomaterials that have found application as antimicrobial agents in several fields. In this review, we summarize some examples of the use of pristine and modified halloysite nanotubes as antimicrobial agents, scaffolds for wound healing and orthopedic implants, fillers for active food packaging, and carriers for pesticides in food pest control.