Although the mineralogical form of occurrence of critical metals is widely recognised as a key factor controlling their recovery during beneficiation, this relationship has rarely been verified directly on freshly mined ore and its primary beneficiation products from Central Asian polymetallic deposits. This raises the research question of how the mineralogical mode of occurrence of Bi, In, Cd, Co, Se, Te and Re governs their distribution between gravity and flotation products. Accordingly, the aim of this study was to establish how the mineralogical form of occurrence of these critical metals determines their distribution among gravity-concentration and flotation products, using ores from the Zhuantobe and Strezhanskoe deposits (Kazakhstan) as a case study. To this end, the mineralogical features and distribution patterns of critical metals during gravity and flotation beneficiation of polymetallic ores from these deposits were investigated by optical microscopy, X-ray diffraction, and SEM-EDS, while metal distribution among beneficiation products was determined by chemical analysis. Sphalerite, galena, pyrrhotite, and silver tellurides were identified as the main carriers of the critical metals, with bismuth occurring as an isomorphic admixture in sphalerite (3.69 wt.%) and galena (1.85 wt.%). During flotation, distribution was governed by mineralogical affinity: cadmium and indium were preferentially concentrated in the zinc concentrate (56.31% and 15.44% recovery, respectively), bismuth in the copper–lead concentrate (23.03%), and selenium and rhenium in the copper-bearing products (23.60% and 37.05%). Correlation analysis of the gravity-concentration products confirmed a close association of cadmium with sphalerite (R² = 0.9998), bismuth with galena and sphalerite (R² = 0.9674), and cobalt with iron-bearing sulfides (R² = 0.9144). These results demonstrate that the distribution of critical metals is governed primarily by their mineralogical form of occurrence rather than by bulk ore content, providing a basis for technologies for the complex processing of polymetallic ores.