Stem cells from the apical papilla (SCAP) are essential for regenerative endodontic treatment. Although mineral trioxide aggregate (MTA) and Biodentine are widely used in regenerative endodontic treatment procedures, their effects on SCAP remain unclear. This study investigated the impact of ProRoot MTA and Biodentine on SCAP viability and mineralization in the presence of Enterococcus faecalis under aerobic and anaerobic environments. Stem cells from the apical papilla were isolated from three healthy donors and exposed to three different surface area-to-volume (SA:V) ratio extracts of ProRoot MTA and Biodentine for 21 days in aerobic or anaerobic conditions. Cell viability was assessed using a neutral red cytotoxicity assay, and mineralization was evaluated by measuring alkaline phosphatase (ALP) activity. No significant differences between ProRoot MTA and Biodentine regarding SCAP viability were detected; however, increased cytotoxicity was found (for both ProRoot MTA and Biodentine) at the highest SA:V ratio of extract used. Oxygen availability, as well as variability in responses of SCAP from the different donors, resulted in greater variation of ALP levels than did type of material. Both ProRoot MTA and Biodentine showed comparable effects on SCAP viability and mineralization, with high SA:V ratios of extracts resulting in increased cytotoxicity. Mineralization in SCAP is influenced by oxygen conditions and the presence of E. faecalis, elucidating the need for further in vivo studies to optimize regenerative endodontic treatment outcomes.