The family Orthomyxoviridae consists of enveloped RNA viruses, including the most common Influenza A virus. The outer shell of the virus is represented by the lipid bilayer with embedded spike glycoproteins and proton channels formed by matrix protein 2 (M2). Underneath the envelope lies the protein scaffold made of matrix protein 1 (M1). This protein also interacts with all eight viral ribonucleoprotein segments (RNPs). Besides protecting viral genome, M1 protein is supposed to play important roles during quite different stages of Influenza virus lifecycle, such as virion disassembly and RNPs release during infection, on the one hand, and proper assembly and budding of new viruses on the other. These processes are known to occur at different pH conditions, so that the function of M1 is also strongly dependent on pH. Therefore, it is of great interest to investigate the structural changes of M1 protein itself and viral protein scaffold under pH changing. For this reason, using atomic force microscopy, we have studied the structure of M1 protein layer formed under its adsorption on charged and hydrophobic surfaces at different ionic strengths and pH conditions as well as the changes of the layer structure under pH changing. It was shown that there is a fundamental difference in the adsorption of M1 protein on the negatively charged surface in neutral compared to acidic conditions. In addition, the acidification resulted in the structural change of the M1 protein layer, thus revealing the possible mechanism of the protein scaffold disassembly.