In this work, we discuss Raman active vibrational and photoluminescence (PL) features of hydrothermally derived cubic phase, manganese selenide (MnSe) quantum dots (QDs) coated with markedly different coating agents, such as, cetyl trimethyl ammonium bromide (CTAB), thioglycolic acid (TGA) and dextran molecules. The homogeneously grown QDs, upon adequate coating, offered a size variation between 5 and 11 nm as evident from imaging through transmission electron microscopy (TEM). The Raman spectra of the QDs have revealed the most prominent peak positioned at ∼680 nm and is ascribed to the third overtone of the longitudinal optical (LO(Γ)) mode. Moreover, the numerous, mixed modes which existed for the uncoated QDs, were found to be suppressed after adequate surface passivation due to surfactant coating. The prominent blue-violet emission response of the MnSe QDs, was seen to be highly symmetric and positioned at ∼428 nm. Furthermore, time resolved PL studies have predicted bi-exponential decay characteristics with a fast component (τ 1 ∼ 0.10 ns) that remains nearly unaffected, but the slow component (τ 2) has varied with the nature of coating agent. In particular, the dextran coated MnSe QDs exhibited a maximal τ 2 value (∼5.5 ns) due to complete surface passivation of the QDs. The influence of surfactants on the vibrational and PL emission parameters of a magneto-fluorescent candidate, like MnSe, would bring new insights for their relevance in nano-photonics and nano-biotechnology to act as active probes for imaging, sensing and targeted therapeutics. • Surface anchored MnSe quantum dots (QDs) have been derived through a rapid hydrothermal route. • Raman active, mixed vibrational modes are found to be suppressed after coating with surfactants. • Highly symmetric, blue-violet emission and positioned at ∼428–430 nm, has been witnessed for all the QD-types. • While fast decay parameter is approximately 0.10 ns, the slow decay component is altered with the nature of coating agent. [ABSTRACT FROM AUTHOR]