- Abstract Expansion of dryland agriculture requires intensive supplement of organic fertilizers to improve the fertility of nutrient-poor desert soils. The environmental impact of organic supplements in hot desert climates is not well understood. We report on seasonal emissions of nitrous oxide (N 2 O) from sand and loess soils, amended with limed and non-limed anaerobic digestate of poultry manure in the Israeli Negev desert. All amended soils had substantially higher N 2 O emissions, particularly during winter applications, compared to unammended soils. Winter emissions from amended loess (10–175 mg N 2 O m − 2 day − 1 ) were markedly higher than winter emissions from amended sand (2–7 mg N 2 O m − 2 day − 1 ). Enumeration of marker genes for nitrification and denitrification suggested that both have contributed to N 2 O emissions according to prevailing environmental conditions. Lime treatment of digested manure inhibited N 2 O emissions regardless of season or soil type, thus reducing the environmental impact of amending desert soils with manure digestate.