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Heterogeneous metal catalysts based on noble metals (Pd, Pt, Rh) are widely used both in industry and in organic synthesis due to their high activity, stability under process conditions and ease of separation from the reaction products. However, their significant drawback is the low selectivity in the formation of the target product, especially when compared with homogeneous metal-complex catalysts. One promising solution to this problem may be the use of bimetallic alloyed catalysts with a highly ordered structure of active centers. In this work the formation of isolated active centers of supported bimetallic Pd-Ag catalysts was studied in detail by a complex of physicochemical methods (CO-FTIR, XRD, TEM). The obtained results showed that the special structure of the active centers of Pd–Ag catalysts could significantly reduce the rate of the second hydrogenation stage (alkene → alkane) of internal alkynes hydrogenation, and also demonstrated higher selectivity rates than the monometallic reference catalyst. In the case of terminal alkynes, the modification with silver does not lead to a significant improvement in the catalytic characteristics, which is due to the high steric availability of the substrate molecule.