Mn-bearing glass phases in metallurgical solid wastes play a crucial yet poorly understood role in regulating the microstructure of cementitious materials. This study investigates how Mn doping influences hydration mechanisms and C-S-H structure in composite cement pastes. Results show that Mn incorporation significantly enhances the dissolution of Si and Al while minimally affecting Ca release, indicating its role as a network modifier that increases glass reactivity under alkaline conditions. Thermal and XRD analyses confirm restrained portlandite accumulation and the dominance of amorphous phases, with no crystalline Mn-bearing products detected. Nanoindentation reveals a fundamental shift in C-S-H packing density: high-density C-S-H decreases substantially while low- and ultra-low-density C-S-H become predominant, leading to a more homogeneous micromechanical response. These findings demonstrate that Mn-bearing phases act as reaction-path regulators rather than densification promoters, steering C-S-H formation toward structurally redistributed, gel-like systems. This mechanistic insight provides a foundation for the targeted utilization of heavy-metal-containing solid wastes in designing low-carbon cementitious materials with tailored microstructures.