After a successful first volume of the Special Issue titled 'Natural compounds as Antimicrobial Agents', we are pleased to publish a second edition, which focuses on specific aspects of this research area, such as the fight against nontuberculous mycobacteria; antimicrobials from toads; apitoxins as antimicrobials; the fight against parasites such as Trypanosomes cruzi or Schistosoma mansoni; the fight against fungi; the use of coral-origin bacteria with antimicrobial volatile compounds; the fight against Clostridium perfringens; the productive effect of L carnitine, which has antimicrobial properties; and the effect of fennel waste extracts against bacteria such as Salmonella, E. coli, or S.aureus in beef burgers.