Tissue regeneration requires an interaction of stem cells and growth factors in a bioactive scaffold. This study utilized the ferret canine as an in situ animal model to investigate a clinically applicable tissue engineering approach for dentin-pulp regeneration. On the other hand, ideal root canal disinfection for dental pulp regeneration is a challenge. There is no study available to address the effect of residual bacteria on the outcome of dental pulp regeneration in previously infected root canals. Therefore, the aim of this study was two-fold: 1) To determine histologically, the efficacy of delivering stem cells within a bioactive scaffold directly into the root canal space compared with the traditional revascularization method and 2) to determine the effect of residual bacteria on the histological and radiographic outcomes of dental pulp regeneration procedures. Periapical lesions were induced in 24 canine teeth of 6 ferrets. Dental pulp stem cells were isolated, characterized, encapsulated in a hydrogel scaffold, and injected in half of the experimental teeth. The other half was treated using the traditional endodontic protocol with a blood clot scaffold. After an evaluation period of 3 months, the animals were sacrificed and block sections were processed for radiographic, histological and histo-bacteriological analyses. Sections were evaluated for the presence/absence of an odontoblast layer, dentin associated mineralized tissue (DAMT), bony islands, intra-canal and periapical inflammation, and bacteria. Data were analyzed using Fisher exact test and one-way analysis of variance (ANOVA) with the p≤0.05. Results of the study showed that there was no significant difference between the traditional and the tissue engineering groups in terms of presence and amount of DAMT and bony islands (p>0.05). Presence of residual bacteria was associated with lack of radiographic growth (p<0.0001) and with presence of intra-canal and periapical inflammation (p<0.05). There was significantly higher amounts of DAMT formed in teeth with no residual bacteria compared to teeth with bacteria (p<0.0001). The results of this study showed that residual bacteria play a critical role in the outcome of regenerative endodontic treatments.