The present work was conducted to investigate the effect of fertilizers {mineral fertilizers (NPK) and organic fertilizer (FYM) and some herbicides (Pendimethalin at the rate of 1.7 l/fed, Prometryn at the rate of 1.0 l/ fed, Metolachlor at the rate of 1.0 l/ fed, Metribuzin at the rate of 300 g/ fed and untreated) on weeds, bacterial nodulation and soil microorganisms associated soybean crop during 2012 and 2013 summer seasons.The results showed that FYM fertilizer significantly increased the dry weight of grassy and broadleaved weeds (g/ m 2 ) after 30 days from sowing. Also, it increased the number and dry weight of nodules/plant, the number of soil microorganisms, pod number /plant, pod weight /plant (g), seeds weight / plant (g), seed yield (ton/ fed.) and NPK seed contents % compared to no fertilizer. This was true in both seasons. All the studied herbicides significantly decreased the dry weight of grassy, broad-leaved weeds and decreased number and dry weight of nodules / plant, number of soil microorganisms and increased pods number /plant, pods weight /plant (g), seeds weight /plant (g), seed yield (ton/fed.) and NPK seed contents % compared to untreated treatment.It can be concluded from this study that application of Pendimethalin at the rate of 1.7 l/ fed and Metribuzin at the rate of 300 g/ fed. with FYM fertilizer were the best for weed control and gave the highest soybean yield.