We report detailed Raman spectroscopic and magnetic susceptibility studies on the spin-driven ferroelectric compounds Mn${}_4$Nb${}_2$O${}_9$ (MNO) and Mn${}_4$Ta${}_2$O${}_9$ (MTO). Both systems exhibit strong spin–phonon coupling below the short-range magnetic ordering temperature ($T_{sro}\sim 220$ K), followed by further anomalous changes in several Raman modes at the long-range magnetic ordering temperatures ($T_N$ = 120 K for MNO and 110 K for MTO). Distinct low-temperature evolutions of Raman mode shift, linewidth, and integrated intensity in MNO and MTO highlight the role of the nonmagnetic cation in tuning spin–lattice coupling, driven by differences in spin–orbit coupling and orbital hybridization between Nb${}^{5+}$ (4$d$) and Ta${}^{5+}$ (5$d$). By combining Raman spectroscopy with nuclear magnetic resonance, and diffuse reflectance spectroscopy, we further show that Mn-based systems possess a more distorted local structure than their Co analogues, while their electronic structures differ despite comparable band gaps. These results provide a comprehensive understanding of spin–lattice coupling in Mn- and Co-based $A_4{X}_2$O${}_9$ ($A$ = Fe, Co, Mn; $X$ = Nb, Ta) magnetoelectric systems.