<p>Selenium-based transition metal chalcogenides (TMC) have a special interest in thermoelectric applications due to their low toxicity and earth abundance and active research is ongoing on the synthesis of transition metal chalcogenides. In the present investigation, we have synthesized CoMSe₂ (Ni, Fe) through direct melting and investigated the low-temperature magnetic and thermoelectric properties. As synthesized CoNiSe₂ (CNS) has antiferromagnetic ordering and exhibits Griffiths-like phase at extremely low temperatures. CoFeSe₂ (CFS) has high-temperature ferrimagnetic behavior with T_C ~ 890.5&#xa0;K. The Fe substitution at the Ni site enhanced electrical conductivity, and Seebeck coefficient and resulted in a PF of 55&#xa0;μW/mK². The improved mobility, density of state near E_F and phonon generation contribute to the improvement in various transport properties in CFS and resulted in 10 times increase in thermoelectric efficiency of the material (ZT). This work provides a new synthesis route for magnetic chalcogenides which are useful for thermoelectric and spintronics applications. The comparatively less explored class of TMCs CoMSe₂ (M = Ni, Fe) exhibits intrinsically low thermal conductivity along with magnetic ordering, offering advantages over conventional high performance thermoelectric materials. Complementary spin-polarized DFT calculations reveal that Fe substitution in CoFeSe₂ enhances the density of states at the Fermi level and transforms the nearly compensated antiferromagnetic ground state of CoNiSe₂ into a ferrimagnetic metallic state, thereby providing a microscopic basis for the observed improvements in transport and magnetic properties. The experimental and theoretical magnetic, thermoelectric investigation opens up multifunctional studies on this class of new materials CoMSe₂.</p>