ε-Polylysine (ε-PL) is a food-grade cationic antimicrobial that is highly effective against a range of food pathogens and spoilage organisms. In compositionally complex environments, like those found in most foods and beverages, the antimicrobial activity of cationic ε-PL is likely to be impacted by its interactions with anionic components. The purpose of this study was to characterize the interactions between cationic ε-polylysine and an anionic biopolymer (high methoxyl pectin, HMP) using isothermal titration calorimetry (ITC), microelectrophoresis (ME), and turbidity measurements. ITC and ME measurements indicated that ε-PL bound to pectin, while turbidity measurements indicated that the complexes formed could be either soluble or insoluble depending on solution composition. Ionic strength and pH were also shown to affect the interactions significantly, highlighting their electrostatic origin. This study demonstrates that ε-PL can form either soluble or insoluble complexes with anionic biopolymers depending on the composition of the system. Our study provides basic knowledge that will facilitate the more rational application of ε-PL in complex food systems.