The esterification reaction of different amino acids with methanol catalyzed by H2SO4 was first studied in the small volume of thin films generated by ESI microdroplet deposition. The reaction is promoted by the pneumatic spray of the ESI source and reaches its maximum efficiency at a thin film temperature of 70 °C. Selective esterification of the COOH moiety was demonstrated. Microdroplet size and thin film volume and lifetime are critical parameters that influenced the reaction outcome. As expected, l-tyrosine and l-phenylalanine having aromatic side chain substituents were the most reactive amino acids, reaching absolute yields of around 40-50%. The amino acid esterification catalyzed by H2SO4 in a thin film occurs under synthetic conditions in which the same reaction in the bulk is not observed.