In this research, hybrid organic-inorganic silica films were applied on the pre-treated AZ91 magnesium alloy by using the dip coating technique. Inorganic precursor, tetraethylorthosilicate (TEOS), and the organic silane, methyltriethoxysilane (MTES), were used for providing a hybrid sol-gel thin-layer film. Different amino acids were incorporated into the coatings, and their corrosion inhibition performance was then investigated by using electrochemical techniques. The results indicate that the addition of l-Alanine, l-Glutamine, l-Methionine, and l-Aspartic amino acids as green inhibitors with a concentration of 0.1, 0.5, 1.0, and 0.5 wt%, respectively to the hybrid silane solution has outstanding inhibition performance. Furthermore, among the amino acids investigated, l-Aspartic exhibits the most improved corrosion resistance. The morphological characteristics of the sol–gel coatings were analyzed by using scanning electron microscopy (SEM). The thickness evaluation of the sol-gel coatings reveals that they are a thin layer with a thickness of about 250 nm. The hydrolysis of sol sample was also characterized by Fourier transform infrared (FT-IR) spectroscopy. The corrosion protection behavior of the coatings was evaluated by using electrochemical impedance spectroscopy (EIS) in 3.5% sodium chloride solution. Finally, DFT calculations were performed to confirm and explain the results obtained from experiments.