A method for removing solid wastes from an organic extractant-based SX/EW copper processing system. A lixivant is initially applied to copper ore, followed by mixing of the copper-containing lixivant product with an organic extractant. The organic extractant (which contains extracted copper ions) is then contacted with an electrolyte solution. At least part of the remaining organic fraction after electrolyte contact is passed through a filtration membrane (either an ultrafiltration or microfiltration membrane) to remove solid wastes. The filtered organic fraction is then reused within the system, followed by electrowinning of the copper-containing electrolyte to recover purified copper. Alternatively, the organic extractant may be membrane-filtered after initial contact with the copper-containing lixivant product to remove solid wastes from the organic extractant. Both embodiments improve phase separation efficiency, reduce organic extractant losses, and improve the effectiveness of the electrowinning process.