Responsible sourcing and processing of critical minerals is the key to effective energy transition. The current traditional extraction of rare earth elements (REEs) from REEs-bearing minerals is carbon-intensive, uses harsh chemicals, and produces a large amount of toxic waste. Therefore, the need for sustainable development of innovative flowsheets to assist the mining industry in extracting REEs with a lower carbon footprint is expected to grow rapidly. To address challenges in conventional biomining due to high levels of salts in process waters, refractory, and low-grade mineral ores/wastes, this study aimed to understand the role of salinity and iron/sulfur (Fe/S) oxidation in monazite bioleaching systems. The results showed that microbially driven dissolution of REEs using the native microbes on non-sterile ore was affected by both the availability of Fe/S as well as increased salinity. The consortium of indigenous microbes on the ore dissolved REEs (Ce, La, Nd, Pr, and Y) up to a final concentration of 40 and 54 mg/L in the presence of 30 and 15 g/L Cl− (as NaCl), respectively.