Fourier transform infrared photoacoustic spectroscopy (FT-IR/PAS) was used to study edible coatings and microorganisms on fruit surfaces (apple and honeydew melon). In the experiment, pregelatinized starch and whey protein concentrate were used to prepare edible coatings, while Saccharomyces cerevisiae, Lactobacillus casei, Escherchia coli, and Staphylococcus aureus were used for microbial study. The spectra obtained from the edible coatings on the apple surface indicate that the FT-IR/PAS technique can effectively distinguish the coating surface and the food substrate by examination of magnitude, phase angle, and generalized two-dimensional (G2D) correlation spectra. Results reported show the first application of FT-IR/PAS to directly differentiate a fruit surface (apple and honeydew melon) with/without microorganisms without elaborate sample preparation. The results demonstrate the potential of FT-IR/PAS to characterize the presence of microorganisms on fruit surfaces.