Gemini surfactants and their interactions with proteins have gained considerable scientific interest, especially when amyloidogenic proteins are taken into account. In this work, the influence of two selected dicationic (gemini) surfactants (3,3'-[1,8-(2,7-dioxaoctane)]bis(1-dodecylimidazolium) chloride and 3,3'-[1,12-(2,11-dioxadodecane)]bis(1-dodecylimidazolium) chloride) on two model proteins, bovine serum albumin (BSA) and hen egg white lysozyme (HEWL), have been investigated. A pronounced and sophisticated influence on BSA structure has been revealed, including a considerable change of protein radius of gyration as well as substantial alteration of its secondary structure. Radius of gyration has been found to rise significantly with addition of surfactants and to fall down for high surfactants concentration. Similarly, a remarkable fall of secondary structure (α-helix content) has been observed, followed by its partial retrieval for high surfactants concentration. A strong aggregation of BSA has been observed for a confined range of surfactants concentrations as well. In case of HEWL-gemini system, on the other hand, the protein-surfactant interaction was found to be weak. Molecular mechanisms explaining such behaviour of protein-surfactant systems have been proposed. The differences of properties of both studied surfactants have also been discussed.