The impact of a hardening accelerator based on C-S-H seeding on the microstructure development and the autogenous shrinkage of low water-to-cement ratio (w/c) mortars is studied. C-S-H seeding leads to a significant refinement of the pore structure at early stages of hydration. In the w/c 0.35 mortar with C-S-H seeding, higher mechanical properties are measured up to 1 d; later the effect of seeding becomes insignificant. On the other hand, in the w/c 0.30 mortar the mechanical properties at later ages were reduced with C-S-H seeding. At the same time, the faster refinement of porosity due to seeding at very early ages leads to faster self-desiccation in all mortars. Consequently, lower RH is reached, which is accompanied by higher autogenous shrinkage of the mortars with C-S-H seeding. As a countermeasure, superabsorbent polymers (SAP) were employed as internal curing agents to reduce self-desiccation and autogenous shrinkage in mortars with seeding agents.