Citric acid-based polymer/hydroxyapatite composites (CABP-HAs) are a novel class of biomimetic composites that have recently attracted significant attention in tissue engineering. The objective of this study was to compare the efficacy of using two different CABP-HAs, poly (1,8-octanediol citrate)-click-HA (POC-Click-HA) and crosslinked urethane-doped polyester-HA (CUPE-HA) as an alternative to autologous tissue grafts in the repair of skeletal defects. CABP-HA disc-shaped scaffolds (65 wt.-% HA with 70% porosity) were used as bare implants without the addition of growth factors or cells to renovate 4 mm diameter rat calvarial defects (n = 72, n = 18 per group). Defects were either left empty (negative control group), or treated with CUPE-HA scaffolds, POC-Click-HA scaffolds, or autologous bone grafts (AB group). Radiological and histological data showed a significant enhancement of osteogenesis in defects treated with CUPE-HA scaffolds when compared to POC-Click-HA scaffolds. Both, POC-Click-HA and CUPE-HA scaffolds, resulted in enhanced bone mineral density, trabecular thickness, and angiogenesis when compared to the control groups at 1, 3, and 6 months post-trauma. These results show the potential of CABP-HA bare implants as biocompatible, osteogenic, and off-shelf-available options in the repair of orthopedic defects.