To assess the effect of biodentine (BD) and MTA‐angelus (MTA) on biocompatibility, BMP2, BMP4, and osteocalcin (OC) expression. Subcutaneously implanted tubes of four groups (MTA, BD, Control, and Sham) were kept over 15, 30, and 60 days; histological analyses were performed using H&E and Von Kossa; ELISA quantified IL‐1β and IL‐8 expression; and qRT‐PCR verified gene expression of BMPs and OC. Sham showed slight changes in profile/intensity of inflammatory infiltrate in all periods. Control had an inflammatory score significantly higher than Sham at 15 days (p < .05). BD revealed a similar inflammatory response to Sham, without significant changes over periods. MTA group exhibited an increase in chronic inflammatory profile at 30 days, with significant reduction at 60 days, when compared to Sham (p < .05). At 30/60 days, experimental groups presented birefringent areas. At 30/60 days, BD and MTA significantly increase IL‐1β compared to Control, whereas an increase in IL‐8 was observed only in BD. At 30/60 days, BD produces an expression of BMP2 whereas MTA influenced BMP4 and OC. Materials tested are biocompatible and they have osteoinductive activity; the materials influenced the expression of the tested mediators differently, suggesting different affinities with the substrate and the dental substrates.