Nanomaterials can enhance interactions with stem cells for tissue regeneration. This study aimed to investigate the biological effects of tricalcium silicate nanoparticle-containing cement (Biodentine™) during or after setting on stem cells from human exfoliated deciduous teeth (SHED) to mimic clinically relevant situations in which materials are adapted. Specimens were divided into four groups depending on the start of extraction time (during (3, 6 and 12 min) or after setting (24 h)) and extracted in culture medium for 24 h for further physicochemical and biological analysis. After cell viability in serially diluted extracts was evaluated, odontogenic differentiation on SHED was evaluated by ARS staining using nontoxic conditions. A physicochemical analysis of extracts or specimens indicated different Ca ion content, pH, and surface chemistry among groups, supporting the possibility of different biological functionalities depending on the extraction starting conditions. Compared to the ‘after setting’ group, all ‘during setting’ groups showed cytotoxicity on SHED. The during setting groups induced more odontogenic differentiation at the nontoxic concentrations compared to the control. Thus, under clinically simulated extract conditions at nontoxic concentrations, Biodentine™ seemed to be a promising odontoblast differentiating biomaterial that is helpful for dental tissue regeneration. In addition, to simulate clinical situations when nanoparticle-containing cement is adjusted, biological effects during setting need to be considered.