Cation substitution is one of the effective ways to improve Cu2ZnSn(S,Se)4 (CZTSSe) photovoltaic performance. However, the commonly reported substitutes, Ag and Cd, are not ideal as they detract from the earth-abundant and nontoxic motivation of CZTSSe. Herein, the role of Mn substitution in sulfide and sulfoselenide films are compared in terms of optoelectronic properties and device performance. CZT(S,Se) + CMZT(S,Se) double-layered structures are fabricated by a sol–gel spin-coating method with variations in the CMZT(S,Se) layer thickness. It is found that a smaller amount of Mn is required to achieve the highest photovoltaic performance in sulfoselenide films in comparison with sulfide-based films. All device parameters (particularly Voc and fill factor) of the sulfoselenide films are improved as compared with the sulfide system. Using a combination of capacitance–voltage, drive-level capacitance profiling, and photoluminescence (PL), it is found that the sulfoselenide film has a smaller interface defect density and higher hole mobility and PL intensity, which suggest much more effective charge separation and transport. In contrast, in double-layer sulfide films, Mn reduces the acceptor defect level of the absorber.