In this paper, prevention of pyrite oxidation by carrier microencapsulation (CME) was investigated. A possible layer structure was suggested following analysis with electrochemical and surface analysis techniques. Electrochemical study of treated pyrite samples showed that treatment with silicon–catechol (Si-Cat) for 6 h at an initial pH of 9.5 gave the best barrier properties and suppression of the samples. Scanning electron microscopy with energy-dispersive X-ray, and Fourier transform infrared (FTIR) analyses confirmed the presence of a silicate layer on the surface of treated pyrite. X-ray photoelectron spectroscopy indicated that the coating layers on the treated pyrite samples consisted of a network of Fe-O-Si and Si-O-Si units bonded to the surface of pyrite. The Si-O-C asymmetric stretching mode was also observed in FTIR spectra. Detailed spectroscopic analyses confirmed the formation of a silicate polymer on a silica–quinone layer, which resulted in the effective suppression effect shown by Si-Cat-treated pyrite at increasing pH.