An accurate assessment of the disease extent and lesion size is needed for appropriate therapy decisions of endodontic-periodontic (endo-perio) lesions. CBCT imaging with less radiation and high spatial resolution can provide a comprehensive evaluation of endo-perio lesions. A total of 71 teeth with endo-perio lesions were assessed using CBCT. Periodontal bone defects were studied for bone loss pattern (horizontal/vertical) along with bone loss levels on mesial and distal sides in association with furcation involvement. The periapical lesions were studied for their prevalence and extent based on CBCT PAI Score. Horizontal and vertical bone loss were detected in 54 teeth (76.1%) and 17 teeth (23.95%), respectively. Mean crestal bone loss levels on mesial and distal aspects were 4.80 ± 3.21 mm and 5.74 ± 3.91 mm, respectively. The mean height, width, and depth of furcation defects were 3.19 ± 2.99 mm, 1.94 ± 0.98 mm, and 4.44 ± 1.92 mm, respectively. Periapical lesions were recorded in 55 teeth (77.5%). A CBCT PAI score of 5 was scored in 35 teeth with a mean lesion diameter of 11.3 ± 2.83 mm, while 16 teeth had healthy periapical tissues (scores of 0 and 1). CBCT is a valuable diagnostic tool that can help assess endo-perio lesions by providing morphometric measurements of periodontal bone defects and the extent of associated periapical lesions.