This pilot study aimed to assess the diagnostic accuracy of CBCT in identifying peri-implantitis-like bone defects in cadavers. Three cadaver dental arches treated with the Thiel embalming method were used. Three different types of peri-implant bone defects (buccal dehiscence, two- to three-wall defects, and circumferential defects) were prepared on 15 implants. Defect depths and lengths were identified clinically using a periodontal probe, radiologically by means of CBCT images, and histologically with a micrometer using an optic microscope. Peri-implant bone defect morphology evaluated using CBCT images matched the clinical defect configuration (100% accuracy). CBCT assessment demonstrated lower values in defect depth and defect length when compared with the clinical evaluation. A statistically significant difference in defect depth (0.35 ± 0.45 mm; P = .037) was recorded between the clinical and CBCT data. Regarding defect length, a statistically significant mean difference of 0.81 ± 0.83 mm (P = .003) was noted between the clinical and CBCT data. Similarly, a mean difference of 1.09 ± 1.52 mm was recorded between the defect length assessed histologically and the CBCT data (P = .031). No statistically significant differences were observed between the other evaluated variables. CBCT is a reliable tool for peri-implantitis diagnosis and treatment planning, though the underestimation of defect severity may affect the prognosis and clinical decision-making. Clinicians need to be flexible in establishing prognoses and treatment based on CBCT assessment.