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The influence of ultrasound and microwaves on extraction of copper, nickel, and cobalt from manganese deep-sea nodules by reductive ammoniacal leaching in the presence of ammonium thiosulfate as a reducing agent was studied. The ultrasonic ammoniacal leaching provides higher metals extraction, while the effect of microwaves on the metals extraction under the studied leaching conditions is insignificant. In general, increasing leaching temperature increases significantly extraction of the metals of interest. At high temperatures, extraction efficiencies of copper, nickel, and cobalt decrease over longer leaching duration as a result of decomposition of the metals amino-complexes and reverse precipitation of metals. However, during the ultrasonic leaching at a temperature of 85 °C, the extraction of nickel remains almost unchanged over longer leaching durations and does not follow the decreasing course, observed in the extraction of copper and cobalt. The finding suggests that nickel can be selectively extracted from the nodules by the ultrasonic leaching. The maximal extraction efficiency of copper, nickel, and cobalt was 83%, 71%, and 32%, respectively, when the reductive ultrasonic ammoniacal leaching was carried out at 85 °C for 90 min. In the presence of microwaves, the maximal extraction efficiency of copper, nickel, and cobalt was 67%, 48%, and 8%, respectively, when the reductive ultrasonic ammoniacal leaching was carried out at the output power of 60 W for 210 min.