This study used pea protein isolate (4% w/w) and kappa-carrageenan (4% w/w) to prepare complex coacervate through electrostatic interactions by optimizing the pH and ratio of protein-to-polysaccharide. The maximum coacervate yield of 81% was achieved at the optimized pH of 3.0 and the protein-to-polysaccharide ratio of 4:1. The optimized coacervate at various concentrations (1, 1.5, 2, 2.5, and 3% w/v) was assessed to emulsify cocoa butter to water fractions. The 2% w/v of complex coacervate successfully emulsified up to 40% aqueous phase in cocoa butter to water fractions whereas complex coacervates at 1%, 1.5%, 2.5%, and 3% w/v were found to stabilize only 20% aqueous phase. The storage and temperature stability of emulsions were higher upon usage of 2% w/v complex coacervate as the serum layer separation was minimal. Based on the emulsion stability observations, complex coacervate (2% w/v) was used to partially and completely substitute lecithin in dark chocolates. The results showed that irrespective of the emulsifiers utilized, the polymorphism and melting behaviour of all chocolates remained the same and retained the desired polymorphic form V. The moisture content and particle size distribution of chocolates did not exceed the acceptable limit. The Casson plastic viscosity (ηca), Casson yield stress (τ0c), and hardness (N) of chocolates significantly (p < 0.05) increased upon increasing the complex coacervate. The present findings revealed that partial substitution (50%) of lecithin with complex coacervate is highly promising for the production of dark chocolates while retaining the desirable flow properties and polymorphism.