Organic amendments not only improve soil conditions but also affect belowground biological processes. This study used a split plot design to investigate the effects of cotton straw management, inorganic fertiliser, and manure amendment on (i) soil nutrient content, (ii) soil microbial properties, and (iii) cotton root growth in a drip-irrigated cotton field. Straw return significantly increased soil inorganic nitrogen (N), N transformation rates, organic carbon (C), and urease activity. Straw return, however, had no significant effect on either root growth or activity. Inorganic fertiliser and/or manure amendment significantly increased inorganic N, N transformation rates, organic C, microbial biomass C, urease activity, and invertase activity. Inorganic fertiliser and/or manure also significantly increased fine root growth, triphenyltetrazolium chloride-reducing capacity, and specific root length. Moreover, the inorganic fertiliser plus manure treatment had the greatest soil inorganic N concentrations, N mineralisation rate, total carbon dioxide efflux, C mineralisation rate, soil organic C concentration, microbial biomass C concentration and enzyme activity, as well as root biomass, fine root : coarse root ratio, root triphenyltetrazolium chloride-reducing capacity and specific root length. Straw return to inorganically fertilised soil increased inorganic N concentrations by 11%, net N mineralisation rate by 59%, net nitrification by 59%, gross nitrification by 14%, denitrification by 39%, and urease activity by 25% compared with inorganic fertiliser alone. Taken together, the results indicated that straw return and manure application significantly promoted soil microbial activity and soil N transformation in the presence of inorganic fertiliser. The manure amendment enabled the crop to develop a more extensive root system, primarily by increasing the number of fine roots. Thus, organic amendments may improve the acquisition efficiency of inorganic fertiliser in drip-irrigated cotton fields.