The SiC/SiOx hetero-superlattice (HSL) consisting of alternating near-stoichiometric SiC barrier layers for the electrical transport and silicon rich SiOx matrix layers for the quantum dot formation is a promising approach to the realization of silicon quantum dot (Si–QD) absorbers for 3rd generation solar cells. However, additional defect states are generated during post deposition annealing needed for the Si–QD formation causing an increase in sub-band gap absorption and a decrease in PL intensity. Proper passivation of excess defects is of major importance for both the optical and electrical properties of the SiC/SiOx HSL Si–QD absorber. In this work, we investigate the effectiveness of the hydrogen reincorporation achieved with hydrogen plasma in a plasma-enhanced chemical vapor deposition (PECVD) reactor, hydrogen dissociation catalysis in hot-wire chemical vapor deposition (HWCVD) reactor and annealing in forming gas atmosphere (FGA). Both the HSL samples and single layer reference samples are tested. The passivation quality of the hydrogen reincorporation was examined by comparing electrical and optical properties measured after deposition, after annealing and after passivation. In addition, the formation of Si–QDs in SiC/SiOx HSL was evaluated using high resolution transmission electron microscopy. We demonstrated that hydrogen can be successfully reincorporated into the annealed HSL sample and its single layer reference samples. FGA passivation is most effective for SiO1.2 single layers and HSL samples. Passivation with PECVD appeared to be only effective for SiC single layers.