Polylysine is a cationic biopolymer with a strong antimicrobial activity against a wide range of microorganisms, however, its functional performance is influenced by its interactions with anionic biopolymers. We examined the stability of polylysine–pectin complexes in the presence of carrageenan, and vice versa. Polylysine–pectin or polylysine–carrageenan complexes were formed at mass ratios of 1:0 to 1:32 (pH 3.5), and then micro-electrophoresis, turbidity, microscopy, and isothermal titration calorimetry (ITC) were used to characterise them. Solutions containing polylysine–pectin complexes were slightly turbid and relatively stable to aggregation at high mass ratios, whereas those containing polylysine–carrageenan complexes were turbid and unstable to aggregation and precipitation. Pectin did not strongly interact with polylysine–carrageenan complexes, whereas carrageenan displaced pectin from polylysine–pectin complexes, which was attributed to differences in electrostatic attraction between polylysine, carrageenan, and pectin. These results have important implications for the design of effective antimicrobial delivery systems for foods and beverages.