The reaction between 2,2′‐bis(3‐aminopyridyl) diselenide (L) and metal transition salts results in the formation of molecular or cluster complexes. The structural elucidation of the synthesized complexes [CuCl2(L)] (1), [Cu(3‐NH2PySeO2)2]·2H2O (2), [Cu4(3‐NH2PySe)4]·dimethylformamide (3), [CoCl2(L)] (4), [ZnCl2(L)] (5), and [Ag6(3‐NH2PySe)6] (6) demonstrates the coordination of nitrogen atoms to CuII, CoII, and ZnII, and that of the selenium atoms to CuIand AgI, which agrees with Pearson’s hard and soft acids and bases (HSAB) theory. Furthermore, the oxidation of selenium with the formation of 3‐aminopyridylseleninate [3‐NH2PySeO2]−bonded to the copper atom was observed in complex2. The antimicrobial action of complexes1,2,4, and5was evaluated againstMycobacterium fortuitum,Mycobacterium massiliense, andMycobacterium abscessus.It was observed that all these complexes have potential antimicrobial activity compared with the free ligand and metal salts used in the synthesis.