Thin film composite polyamide membranes (TFC-PAs) are used commercially in filtration processes, while, less flux at low pressure and high fouling tendency limit their widespread utility. Herein, for the first time, we uncover deep eutectic solvents (DESs) as multi-tasking agents for surface engineering and cleaning of a TFC-PA membrane via a simple and sustainable approach. Upon treatment of TFC-PA with DESs at low temperature (30–50 °C), a remarkable increase in the flux rate (2–5 fold higher than pristine TFC-PA) was achieved without substantial changes in the rejection efficiencies of the solutes. The increase in the flux rate was due to the enhanced surface wettability of the DES treated membranes, which well supported the improved surface smoothness of the TFC-PA membrane after DES treatment. The molecular docking study showed the presence of H-bonding with DES and a polyamide moiety which may help improve the surface smoothness of the TFC-PA membrane during DES treatment. The zeta potential study showed that significant changes occur in the surface charges of the DES treated TFC-PA membrane compared to the control membrane, which suggested a modification of the chemical environment of TFC-PA via H-bonding interactions during DES treatment. Moreover, long-term (time = 250 h and feed = 10 000 ppm humic acid) studies revealed that compared to the water washed TFC-PA membrane, the DES washed membrane showed high flux recovery without compromising the flux boosting potential and rejection of humic acid. Therefore, DESs can be envisaged as both flux promoting and surface cleaning agents for TFC-PA membranes via a cost-effective and eco-friendly approach.