Background and Objectives: Cone Beam Computed Tomography (CBCT) offers high-resolution, three-dimensional imaging for detecting apical periodontitis (AP) and evaluating the technical quality of endodontic treatments. This study aimed to investigate the diagnostic value of CBCT in identifying endodontic failures and periapical lesions and to explore the clinical patterns associated with these findings in a Romanian patient cohort. Materials and Methods: A retrospective study was conducted on 258 patients (with 876 root canal-treated teeth), all of whom underwent CBCT imaging between October 2024 and April 2025 at a private radiology center in Craiova, Romania. Of the 876 treated teeth, 409 were diagnosed with apical periodontitis. Patients were present for endodontic treatment at the Endodontics Clinic of the Faculty of Dentistry, University of Medicine and Pharmacy of Craiova. With the patients’ consent, 3D radiological examinations were recommended for better case planning and accurate diagnosis. The periapical status and technical parameters of root canal fillings were assessed using the CBCT-PAI index and evaluated by three calibrated observers. Associations with demographic, clinical, and behavioral factors were statistically analyzed. Results: Apical periodontitis was detected in 46.69% of the teeth examined during the study period, with CBCT-PAI score 3 being the most prevalent. Poor root canal obturation quality (underfilling, overfilling, and voids) was significantly associated with periapical pathology. Chronic lesions were more common than acute ones, especially in older patients. The number of teeth with endodontic treatments and no AP, as well as the number of teeth with AP, was significantly lower for patients with acute AP, indicating the more severe impact of chronic AP on the patients’ oral health status. CBCT allowed the precise localization of missed canals and assessment of lesion severity. Conclusions: Within the limits of a retrospective, referral-based cohort, CBCT aided the detection of periapical pathology in root canal-treated teeth (46.69%). These findings do not represent population-based rates but support the selective use of CBCT, in line with current ESE guidance, for complex cases or when conventional imaging is inconclusive.