The enhancement of hydrophilicity of DC air and oxygen plasma treated cotton fabric and its effect on the antimicrobial efficacy when treated with neem leaf extract is reported in this paper. The axial and radial ion density distribution between the electrodes was studied using Langmuir probe to place the fabric between the electrodes for effective plasma treatment. The effect of system parameters viz., process gas pressure, DC power density and plasma exposure time on the hydrophilicity and hence the antimicrobial efficacy after the neem leaf extract treatment was analysed and optimised. The functional group present in the cellulose units of the cotton fabric before and after plasma treatment was identified and estimated using standard tests and analysed using ATR-FTIR spectra. The surface morphology of untreated and plasma treated cotton fabric was analyzed with the help of SEM micrograph. The mean pore diameter of the fabric matrix was calculated and air permeability was measured before and after plasma treatment to account for the improved capillarity due to plasma treatment. The formation of functional groups with increased polarity and improved capillary action of the plasma treated fabric enhances its hydrophilicity which in turn improves the sorption of neem leaf extract and hence the antimicrobial activity.