This study explores the enhancement in magnetic and photoluminescence properties of Mn2+‐doped (CdSe)13 nanoclusters, significantly influenced by the introduction of paramagnetic centers through doping, facilitated by optimized precursor chemistry and precisely controlled surface ligand interactions. Using a cost‐effective and scalable synthesis approach with elemental Se and NaBH4 (Se‐NaBH4) in n‐octylamine, we tailored bonding configurations (Cd‐O, Cd‐N, and Cd‐Se) on the surface of nanoclusters, as confirmed by EXAFS analysis. These bonding configurations allowed for tunable Mn2+‐doping with tetrahedral coordination, further stabilized by hydrogen‐bonded acetate ligands, as evidenced by 13C NMR and IR spectroscopy. Mulliken charge analysis indicates that the charge redistribution on Se2‐ suggests electron transfer between surface ligands and the nanocluster, contributing to spin fluctuations. These tailored configurations markedly increased the nanoclusters' magnetic susceptibility and photoluminescence efficiency. The resulting nanoclusters demonstrated a clear concentration‐dependent response in emission lifetimes and intensities upon exposure to magnetic field effects (MFE) and spin‐spin coupling, alongside a large magnetic moment exceeding 40 μB at 180K. These findings highlight the potential of these nanoclusters for magneto‐optical devices and spintronic applications, showcasing their tunable magnetic properties and exciton dynamics.