Effect of severe drought events in combination with organic amendments (municipal solid waste, MSW, sheep manure, SM, and cow manure, CM) on soil dehydrogenase, urease, β‐glucosidase and phosphatase activities and microbial community by analyzing phospholipid fatty acids was studied under controlled laboratory conditions for one year. Two levels of irrigation were used: (1) watered soils, where the soils were maintained at 60% of their water holding capacity through the experiment, and (2) non‐watered soils, without irrigation through the experiment. The severe drought conditions negatively affected the soil enzymatic activities and total bacterial and fungal PLFA concentrations. The application of organic amendments to the soil subjected to severe drought increased soil water retention and encouraged the growth and activity of soil microbial populations. However, the chemical composition of the organic matter applied to the soil also strongly influenced soil moisture. In non‐watered soils and compared with the unamended soil, the dehydrogenase activity was 71 · 3%, 60 · 9% and 38 · 6% higher in the soil with SM, CM and MSW, respectively. Urease activity was 60 · 6%, 51 · 5% and 37% higher in the soil with SM, CM and MSW, respectively. β‐glucosidase and phosphatase activities had a similar trend. Water retention was higher when the organic wastes applied to the soils had a higher content of humic acids than fulvic acid contents. Copyright © 2016 John Wiley & Sons, Ltd.