We analysed the antimicrobial and antioxidant activities of phenolic metabolites secreted from a naringenin-producing Saccharomyces cerevisiae strain (a GRAS organism), against the pure flavonoid naringenin and its prenylated derivatives, to assess their potential as natural food preservatives. Agar disc diffusion assay was used to analyse the antimicrobial activity against Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 29213, while DMPD chemiluminescence assay was used to analyse antioxidant activity, based on DMPD+-scavenging activity. Our results showed that the engineered yeast metabolites exhibited both strong antimicrobial and DMPD+-scavenging activity, particularly the metabolite phenylacetaldehyde. Pure naringenin had poor antimicrobial and DMPD+-scavenging effects. Prenylated varieties, 6-prenylnaringenin and 8-prenylnaringenin, inhibited only S. aureus, while only 8-prenylnaringenin exhibited moderate DMPD+-scavenging activity. Our results suggested that phenolic metabolites secreted from naringenin-producing yeast would be a sustainable source of natural food preservatives.