There is increasing interest in the use of organic amendments in the Australian cotton ('Gossypium hirsutum L.') industry because of perceived benefits to soil health and the environment. A 2-year field experiment was conducted at the Australian Cotton Research Institute (ACRI), near Narrabri, NSW, using three locally available organic amendments applied at typical farmers’ rates to irrigated cotton. The amendments used were cattle manure (10 t/ha), composted cotton gin trash (7.5 t/ha), and a commercial liquefied vermicompost (50 L/ha), and their effects on soil quality characteristics were compared with those of control soil where no amendment was added. The soil (0–0.10 m) was sampled on six occasions and analysed for selected chemical and microbiological properties. The physiological characteristics and nutrient uptake of mature cotton plants were also examined. The organic amendments did not have a significant effect on microbiological properties as measured by microbial biomass and respiration. Of the chemical properties measured, manure-amended plots showed higher nitrate-nitrogen, available phosphorus, and exchangeable potassium (K) concentrations over 2 years. Exchangeable K was 28% higher where cattle manure was applied than in control plots during the active growth stage of cotton in the first year of experiment. Higher nutrient uptake by mature cotton plants and lower nutrient concentration in soil were observed in the second year. Cotton physiological properties and lint yield were not significantly affected by the application of organic amendments. Seasonal parameters had a strong effect. The results suggest that there are few short-term benefits to be gained in terms of soil quality from application of organic amendments to Vertosols at the rates used in these trials.