Recently, our group developed two different polymeric biomaterials with photodynamic antimicrobial surface activity for periodontal bone regeneration. The aim of the present study was to analyze the biocompatibility and osseointegration of these materials in vivo. Two biomaterials based on urethane dimethacrylate (BioM1) and tri-armed oligoester-urethane methacrylate (BioM2) that additionally contained ß-tricalcium phosphate and the photosensitizer mTHPC (meso-tetra(hydroxyphenyl)chlorin) were implanted in non-critical size bone defects in the femur (n = 16) and tibia (n = 8) of eight female domestic sheep. Bone specimens were harvested and histomorphometrically analyzed after 12 months. BioM1 degraded to a lower extent which resulted in a mean remnant square size of 17.4 mm², while 12.2 mm² was estimated for BioM2 (p = 0.007). For BioM1, a total percentage of new formed bone by 30.3% was found which was significant higher compared to BioM2 (8.4%, p < 0.001). Furthermore, BioM1 was afflicted by significant lower soft tissue formation (3.3%) as compared to BioM2 (29.5%). Additionally, a bone-to-biomaterial ratio of 81.9% was detected for BioM1, while 8.5% was recorded for BioM2. Implantation of BioM2 caused accumulation of inflammatory cells and led to fibrous encapsulation. BioM1 (photosensitizer-armed urethane dimethacrylate) showed favorable regenerative characteristics and can be recommended for further studies.