Two new coordination compounds comprising Mn(II) and Cu(II) viz. [Mn(bz)2(Hdmpz)2(H2O)] (1) and [Cu(crot)2(Hdmpz)2] (2) (where, bz = benzoate; crot = crotonate; Hdmpz = 3, 5-dimethyl pyrazole) were synthesized and characterized. The characterization involved a single crystal X-ray diffraction technique, FT-IR spectroscopy, electronic spectroscopy, TGA, and elemental analyses. Compounds 1 and 2 crystallize as mononuclear entities of Hdmpz with penta-coordinated Mn(II) and hexa-coordinated Cu(II), respectively. These complexes exhibit distorted trigonal bipyramidal and distorted octahedral geometries, respectively. A crystal structure analysis of compound 1 elucidates the existence of C–H⋯π and π-stacking interactions alongside O–H⋯O, N–H⋯O, and C–H⋯O H-bonding interactions contributing to the stabilization of the compound’s layered assembly. Similarly, in compound 2, the crystal structure stability is attributed to the presence of hydrogen bonding in conjugation with π-stacking interactions. We conducted theoretical investigations to analyze π⋯π, H-bonding, and antiparallel CH···π non-covalent interactions observed in compounds 1 and 2. DFT calculations were performed to find out the strength of these interactions energetically. Moreover, QTAIM and non-covalent interaction (NCI) plot index theoretical tools were employed to characterize them and evaluate the contribution of the H-bonds.