Green coffee chlorogenic acids (CGA) and dodecyl chlorogenates (DCGA) were screened for their in vitro antimicrobial activity on different bacterial strains (Bacillus cereus, Clostridium sporogenes, Listeria innocua, Micrococcus luteus, Staphylococcus aureus, Escherichia coli, Pseudomonas fluorescens, Salmonella enterica), and for their antifungal and anti-mycotoxigenic activities against Aspergillus flavus and A. ochraceus. Sa. enterica was resistant to both CGA and DCGA. CGA had an antimicrobial effect on gram-positive and gram-negative bacteria; it exhibited bactericidal activity against P. fluorescens and S. aureus, and had no sporicidal activity against B. cereus and C. sporogenes. DCGA was active on three grampositive bacteria and inactive on the gram-negative ones. Both, CGA and DCGA presented anti-Aspergillus activities and were better anti-mycotoxigenic agents for ochratoxin A than for aflatoxin B1. This work reports for the first time both CGA and DCGA as antibacterial, antifungal and anti-mycotoxigenic agents, which could be promising preservatives in food or nonfood products.