The impact that the anion and alkyl group has on the electronic structures and magnetic properties of four mononuclear Mn(III) complexes is explored in [Mn(salEen-Br)$_2$]Y (salEen-Br = 2-{[2-(ethylamino)ethylimino]methyl}-4-Br-phenol; Y = ClO$_4$$^–$ 1 and BF$_4$$^–$·1/3CH$_2$Cl$_2$ 2) and [Mn(salBzen-Br)$_2$]Y (salBzen-Br = 2-{[2-(benzylamino)ethylimino]methyl}-4-Br-phenol; Y = ClO$_4$$^–$ 3 and BF$_4$$^–$ 4). X-ray structures of [Mn(salEen-Br)$_2$]ClO$_4$$^–$·0.45C$_6$H$_{14}$ 1-hexane, [Mn(salEen-Br)$_2$]BF$_4$·0.33CH$_2$Cl$_2$·0.15C$_6$H$_{14}$ 2-dcm-hexane, and 3–4 reveal that they crystallize in ambient conditions in the monoclinic P2$_1$/c space group. Lowering the temperature, 2-dcm-hexane uniquely exhibits a structural phase transition toward a monoclinic P2$_1$/n crystal structure determined at 100 K with the unit cell trebling in size. Remarkably, at room temperature, the axially elongated Jahn–Teller axis in 2-dcm-hexane is poorly defined but becomes clearer at low temperature after the phase transition. Magnetic susceptibility measurements of 1–4 reveal that only 3 and 4 show slow relaxation of magnetization with Δ$_{eff}$/$k_B$ = 27.9 and 20.7 K, implying that the benzyl group is important for observing single-molecule magnet (SMM) properties. Theoretical calculations demonstrate that the alkyl group subtly influences the orbital levels and therefore very likely the observed SMM properties.