Chitosan, a cationic biopolymer is a major derivative of chitin. It is biocompatible, non-toxic and environ-friendly material and has broad spectrum antimicrobial activity. However, it is less effective in neutral or basic conditions due to its solubility only in acidic medium. Therefore, chemical modification with suitable groups is necessary to enhance the potency of chitosan. The present study was mainly conducted to explore the effect of structural modifications on antimicrobial potential of chitosan. N-Methyl, N-Ethyl and N-Propyl pyrrole were reacted with N-chloroacyl-6-O-triphenylmethylchitosan prepared by stepwise modification of chitosan to form N-Methyl, N-Ethyl and N-Propyl pyrrole derivatives of chitosan. Structural characterization of these pyrrole derivatives was done by IR, NMR, XRD, DSC and Elemental Analysis. The gram-negative bacterium Escherichia coli, gram-positive bacterium Staphylococcus aureus were selected for antibacterial activity and the fungus C. albicans was selected for antifungal activity by agar diffusion method and MIC method. Antimicrobial activity of the N-Methyl, N-Ethyl and N-Propyl pyrrole derivatives on E. coli, S. aureus and C. albicans showed an inhibitory effect on all the organisms. The potency of inhibition was found to be varied with the substitutions. The maximum activity was shown by N-pyrrolylpropylchitosan against E. coli (zone of inhibition 1.2±0.05cm, MIC 0.15±0.03mg/ml), S. aureus (zone of inhibition 1.4±0.03cm, MIC 0.15±0.01mg/ml), C. albicans (zone of inhibition 0.8±0.03cm, MIC 0.2±0.03mg/ml). The study also confirmed that all the three derivatives exhibited higher inhibition than that of chitosan against E. coli (zone of inhibition 0.7±0.03cm, MIC 0.09±0.02mg/ml), S. aureus (zone of inhibition 0.8±0.03cm, MIC 0.09±0.02mg/ml), C. albicans (zone of inhibition 0.6±0.03cm, MIC 0.09±0.03mg/ml). Results demonstrated that these three N-alkylpyrrole chitosan derivatives exhibited improved potency and hence can have the more applicability as antimicrobials.