This report describes the synthesis of two ruthenium(II) ENE pincer complexes (E = S, C1 and E = Se, C2) by the reaction of bis(2‐(phenylchalcogenyl)ethyl)amine (L1, L2) with RuCl2(PPh3)3. The complexes were characterized with the help of 1H and 13C{1H} NMR, FTIR, HRMS, cyclic voltammetry and elemental analysis techniques. The structure and bonding mode of ligand with ruthenium in C2 was established with the help of single crystal X‐ray diffraction. The complex showed distorted octahedral geometry with two chlorine atoms trans to each other. The Ru−Se bond distances (Å) are 2.4564(3)‐2.4630(3), Ru−N distance is 2.181(2), Ru−P distance is 2.2999(6), and Ru−Cl distances are 2.4078(6)‐2.4314(6). The complexes showed good to excellent catalytic activity for the N‐alkylation of o‐phenylenediamine with benzyl alcohol derivatives to synthesize 1,2‐disubstituted benzimidazole derivatives. The complexes were also found to be efficient for aerobic oxidation of benzyl alcohols to corresponding aldehydes which are precursors to the bisimines generated in situ during the synthesis of 1,2‐disubstituted benzimidazole derivatives. Complex C2 where selenium is coordinated with ruthenium was found to be more efficient as compared to sulfur coordinated ruthenium complex C1. Since ruthenium complexes are getting increasing attention for developing new anticancer agents, the preliminary studies like binding behavior of both the complexes towards CT‐DNA were studied by competitive binding with ethidium bromide (EthBr) using emission spectroscopy. In addition, the interactions of C1−C2 were also studied with bovine serum albumin (BSA) using steady state fluorescence quenching and synchronous fluorescence studies. A good stability of Ru(II) state was observed by cyclic voltammetric studies of C1−C2. Overall these molecules are good examples of bio‐organometallic systems for catalytic and biological applications.