This study explores the aggregation properties and interfacial behavior of imidazolium-based ionic liquids [C14mim][Br] and [C15mim][Br], in the presence of the dipeptide glycyl-L-alanine at varying concentrations (0.20, 0.40, 0.60 mol/kg) in aqueous media. Conductivity and surface tension measurements were conducted to determine the critical micelle concentration (CMC) and associated interfacial parameters. The results indicate that the addition of the dipeptide significantly reduces the CMC of both ILs, suggesting enhanced micellization. This behavior is attributed to electrostatic interactions and ion-pair formation between IL head groups and dipeptide molecules. The CMC of ionic liquids increases with temperature. This is because of weakening or disruption of hydrogen bonding between ionic liquid head groups and dipeptide molecule, which diminishes the stabilizing interactions, required for aggregation, thereby hindering micellization. Thermodynamic analysis confirms that micellization is a spontaneous and exothermic process. The Gibbs free energy of micellization (ΔG°m) becomes increasingly negative with higher dipeptide concentrations, further supporting the enhancement of micellization. Furthermore, surface excess concentration (Γmax) values were found to be positive, demonstrating reduced surface tension upon IL adsorption. Simultaneously, minimum area per molecule (Amin) increased, suggesting looser molecular packing at the interface. The more negative Gibbs free energy of adsorption (ΔG°ad) compared to ΔG°m suggests that adsorption at the air–water interface is thermodynamically favored over micellization. This study provides a systematic evaluation of the influence of a dipeptide on the micellization thermodynamics of imidazolium-based ILs, offering valuable insights into peptide–surfactant interactions in aqueous systems.