Geochemistry of chlorine and fluorine in apatites, micas, and amphiboles in rocks from eight intrusive complexes of the Siberian Platform has been first studied on the basis of new factual and analytical data (more than 1000 analyses). The main attention is focused on minerals from layered intrusions. Most apatites show F > Cl; the maximum contents of halogens are specific to chlorapatite (6.97 wt.% Cl) and fluorapatite (6.04 wt.% F). The total f value (f = Fe/(Fe + Mg), at.%) of femic minerals varies from 2 to 98 at.% in micas and from 22 to 95 at.% in amphiboles. The Cl–f and F–f trends show an increase in the Cl content and a decrease in the F content in the minerals with increasing f. Chlorine clearly exhibits ferrophilic properties, and fluorine has magnesiophilic properties. The halogen-richest minerals are fluorophlogopite (F = 7.06 wt.%, f = 7 at.%), chlorannite (Cl = 6.30 wt.%, f = 89 at.%), and chloroferrihastingsite (Cl = 5.22 wt.%, f = 90 at.%). Coexisting micas and amphiboles in the rocks are close in f value, but the micas are richer in Cl than the amphiboles. We assume that the halogen-containing minerals crystallized at the high pressure of halogen–hydrocarbon fluids at the levels of the MW, IW, and QIF buffers. The reducing conditions of the magmatism process are also evidenced by the presence of graphite and native metals in the rocks. The similarity of the Cl–f and F–f trends of micas and amphiboles from different intrusive complexes indicates the same mechanisms of the melt differentiation and mineral crystallization.