The primary focus of catalytic chemistry is the synthesis of valuable chemicals from cheaper and more abundant substrates. The main objective of catalytic processes is to achieve higher yields at affordable costs under environmentally friendly conditions. Under homogeneous conditions, the synthesized bimetallic Mn(II) complex with (2-benzoylbenzoic acid, bba) and N,N coordinated (2,2-bipyridine, bipy) ligands, [Mn2(μ1,3-(C6H5)CO(C6H4)COO)2(bipy)2].2ClO4 is shown to be an active catalyst for the oxidation of monoterpenes (thymol and carvacrol), using TBHP under mild reaction conditions. The structure of the complex was characterized by single-crystal X-ray diffraction. The six-coordinated Mn(II) centers bridge in a coordination pattern due to the monodentate bonding mode of the carboxylate oxygen atoms of benzoylbenzoate anion. The selectivity of the Mn-catalyst was measured to be 100 % for thymol and carvacrol to thymoquinone. A simple, effective and selective Mn(II)/TBHP/Monoterpene/CH3CN catalyst system was used for the oxidation of thymol (TOF = 2000 h−1, in 15 min) and carvacrol (TOF = 667 h−1, in 45 min.) into a valuable product, thymoquinone (TQ), in acetonitrile at 80 °C.