The disposal of dyes and organic matter into water bodies has become a significant source of pollution, posing health risks to humans worldwide. With rising water demands and dwindling supplies, these harmful compounds must be isolated from wastewater and kept out of the aquatic environment. In the research presented here, hydrothermal synthesis of manganese-doped zinc ferrites’ (Mn-ZnFe2O4) nanoparticles (NPs) and their nanocomposites (NCs) with sulfur-doped graphitic carbon nitride (Mn-ZnFe2O4/S-g-C3N4) are described. The samples’ morphological, structural, and bonding features were investigated using SEM, XRD, and FTIR techniques. A two-phase photocatalytic degradation study of (0.5, 1, 3, 5, 7, 9, and 11 wt.%) Mn-doped ZnFe2O4 NPs and Mn-ZnFe2O4/(10, 30, 50, 60, and 70 wt.%) S-g-C3N4 NCs against MB was carried out to find the photocatalyst with maximum efficiency. The 9% Mn-ZnFe2O4 NPs and Mn-ZnFe2O4/50% S-g-C3N4 NCs exhibited the best photocatalyst efficiency in phase one and phased two, respectively. The enhanced photocatalytic activity of the Mn-ZnFe2O4/50% S-g-C3N4 NCs could be attributed to synergistic interactions at the Mn-ZnFe2O4/50% S-g-C3N4 NCs interface that resulted in a more effective transfer and separation of photo-induced charges. Therefore, it is efficient, affordable, and ecologically secure to modify ZnFe2O4 by doping with Mn and homogenizing with S-g-C3N4. As a result, our current research suggests that the synthetic ternary hybrid Mn-ZnFe2O4/50% S-g-C3N4 NCs may be an effective photocatalytic system for degrading organic pollutants from wastewater.