To address the insolubility of x(SiO2)·GeO2 and y(Fe3O4)·GeO2, this study introduced a two-step leaching (NaOH leaching-NL and low-temperature molten NaOH leaching- LTMNL) method. During the NL process, 51.30 % of germanium (Ge), 84.96 % of aluminum (Al), and 56.45 % of silicon (Si) were leached. Moreover, in the LTMNL process, over 97.43 % of Ge and nearly all amphoteric metals (e.g., Al, Zn, and As) were dissolved under optimized conditions (including a NaNO3-to-ore mass ratio of 0.15, leaching temperature of 170 °C, alkali-to-ore mass ratio of 10, agitation speed of 500 rpm, and reaction time of 2 h). The leachate obtained from the LTMNL process was used as a lixiviant in the NL process to facilitate the recyclable utilization of NaOH and enrich Ge in the leachate solution. This approach resulted in an overall germanium recovery efficiency of 98.72 %. The germanium concentration in the NL leachate exceeded 400 mg/L, thereby facilitating subsequent germanium recovery. Additionally, the LTMNL residue, containing an iron concentration of 52.46 wt%, served as an iron resource. Therefore, the two-step leaching process achieved high germanium recovery and efficient separation of Ge and Fe compared with conventional H2SO4 leaching methods. This indicates that the two-step leaching process is a promising and efficient method for treating germanium-bearing material in the form of x(SiO2)·GeO2 and y(Fe3O4)·GeO2).