Porphyromonas gingivalis is a notorious keystone periodontal pathogen. However, it is difficult to selectively inhibit its growth in the oral cavity. Thereby, liposome-based antibacterial agents were investigated to suppress the growth of P. gingivalis. The antibacterial activities of enzymatically prepared lysolecithin-free fatty acid liposomes were comparable to those of free-form linoleic acid in a simple aqueous system with minimum inhibitory concentration (MIC) of 4.8 μg/mL. However, this value was 2.8-fold lower than those of the lecithin liposomes including the same amount of free fatty acids (e.g., linoleic acid). This indicated that the lysolecithin liposomes are very efficient in delivery of free fatty acids from the aqueous medium to P. gingivalis. Remarkably, the antibacterial activities in the presence of milk and milk alternatives were significantly stronger (MIC, 35 μg/mL) than free-form linoleic acid (MIC, ≥100 μg/mL). The higher antibacterial activities of the liposomal fatty acids might be due to efficient delivery of the antibacterial fatty acids from the liposomes to P. gingivalis even in the presence of emulsified fat globules and protein micelles in milk and milk substitutes. Besides, the lysolecithin-free fatty acid liposomes hardly inhibited growth of Gram (+) bacteria including the oral probiotics (e.g., Lactobacillus reuteri). Overall, we envisage that the lysolecithin liposomes may serve as an excellent nano-scale delivery system of multi-functional free fatty acids to targets in complex food systems.