Field experiments were conducted during winter seasons of 2008–09 and 2009–10 at Eastern Block Farm, Tamil Nadu Agricultural University, Coimbatore to study the efficiency of new formulation pre-emergence herbicide pendimethalin 38.7% on growth and development of cotton to ensure the better weed management in a cost effective manner. Pendimethalin 38.7% was tried in four different doses viz., 1.5, 2.0, 2.5 and 4.0 kg/ha and it was compared with pendimethalin 30% @ 1.0 kg/ha, early post-emergence herbicide trifloxysulfuron, power weeders and hand weeding. The experimental results revealed that the herbicides exerted a significant detrimental effect on soil bacteria, fungi and actinomycetes. The counts of bacteria, fungus and actinomycetes recorded at 3 DAHS revealed that soil microbes were more sensitive to pendimethalin (38.7%) 1.5, 2.0, 2.5 and 4.0 kg/ha and pendimethalin (30%) 1.0 kg/ha as evident from significant reduction in their population on 15 and 30 DAHS, eventually microbial density started to recover slowly.