The well-known anti-infective properties of propolis are determined by its chemical composition, which in turn is influenced by geographical factors and reflects the botanical diversity in the vicinity of the beehive. Although there are several reports on the anti-infective properties of crude propolis, few are aimed at identifying specific compound(s) responsible for the observed activities. Using South African propolis as an example, the application of high performance thin layer chromatography-bioautography in tandem with mass spectrometry was investigated for the rapid identification of antimicrobial and anti-quorum sensing (anti-QS) compounds. Pinocembrin was found to be responsible for the observed antifungal activity of the propolis against Candida albicans. Three compounds were found to be active against all of the evaluated Gram-positive and Gram-negative bacteria. The identity of the first was confirmed as pinobanksin, one remains unidentified, while the third corresponds to either pinobanksin 3-O-pentanoate or 2-methylbutyrate. The identification of caffeic acid as the anti-QS component was confirmed quantitatively using the violacein inhibitory assay.