Focusing on the selective extraction of the critical raw materials indium and germanium from real bioleaching solutions, extended studies have been carried out using Europe’s first underground hybrid membrane pilot plant (TRL6). In order to transfer former laboratory experiments to pilot scale, NF99 (Alfa Laval) was used for the evaluation of membrane permeance and ion retention. A performance test of microfiltration (MF) and nanofiltration (NF) showed high permeances with low root-mean-square deviation under feed variation (5.2% for MF, 4.7% for NF). Depending on the feed load, a significant permeance drop of up to 57% for MF (3 bar) and 26% for NF (10 bar, 1.1 m s−1) was observed. The NF retention performance showed that, without regular chemical cleaning, the selectivity between the target elements degraded. By introducing acidic-basic cleaning steps, it was possible to keep the retention behavior at an approximately constant level (In 91.0 ± 1.3%; Ge 18.2 ± 5.5%). In relation to the specified target, the best results could be achieved at low pressure (7.5 bar) and a maximum overflow velocity of 1.1 m s−1, with a retention of 88.4% for indium and 8.8% for germanium. Moreover, the investigations proved the functionality and long-term stability of the underground membrane device.