This study investigates various decomposition methods for tungsten-molybdenum ores—wet, dry, and autoclave—to identify optimal conditions for Mo and W extraction. Four ore samples were examined: two reference materials and two natural samples from Central Kazakhstan. Natural samples О-3 and O-4, classified as refractory silica-rich tungsten-molybdenum ores, have complex mineralogical compositions. Optimal decomposition conditions for these ores were established for the first time, considering their geochemical features. X-ray fluorescence (XRF) and X-ray diffraction (XRD) were used to determine the elemental and phase composition, while ICP-MS analyzed digested solutions. The efficiency of Mo and W extraction depend on both mineralogical form and matrix. Nine decomposition methods were tested. For standard molybdenum–tungsten ore samples (O-1 and O-2), the highest recoveries were achieved using acid-based techniques, particularly autoclave digestion with HNO3-HF and wet digestion with HNO₃. In contrast, natural samples with complex silica-rich matrices containing Al, Fe, and Ca (O-3 and O-4) required stronger approaches such as autoclave treatment with HNO3-HF or HCl and alkaline sintering with Na2CO3 followed by HNO3 dissolution. All experiments were performed in triplicate, with a standard deviation of 3–5%. These findings demonstrate the importance of matching decomposition strategies to ore characteristics for effective Mo and W recovery.