Concern in environment-friendly textile processing techniques has been augmenting in recent years. Natural products are environment friendly, low toxic and less allergenic owing to the presence of large number of structurally diverse active compounds which makes natural agents as promising options for the development of antimicrobial protective textiles. The purpose of the present study was to investigate the effect of lemon peel treatment on microbial resistant property of cotton fabric. It was found that the cotton fabric treated with lemon peel extract showed 97.89, 98 and 97.16 percent reduction in the growth of P. aeruginosa, E. coli and X. campestris bacteria, 93.49 and 95.83 percent reduction in the growth of B. subtilis and S. aureus bacteria whereas treated fabric showed 94.99, 90.41 and 93.44 percent reduction against A. clavatus, A. flavus and A. awamori fungal strains, respectively. Lemon peel extract treated cotton fabric was further characterized by FESEM and FTIR spectra to study the changes occurred in the fibre structure after treatment.